Contacts of the helix formed by residues 80 - 102 (chain A) in PDB entry 5IWS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY* 3.5 10.4 + - - +
77A ALA* 2.9 17.9 + - - +
78A LYS* 3.2 40.4 - - - +
79A ASP* 1.3 79.3 - - - +
81A ALA* 1.3 65.1 + - - +
82A GLY 3.2 1.6 + - - +
83A GLY* 3.3 9.9 + - - -
84A ALA* 3.6 6.1 + - - +
157A TYR* 3.9 28.7 - - + +
158A ASN* 2.8 33.4 + - - +
161A TYR* 3.3 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP 4.1 1.6 + - - -
80A ARG* 1.3 72.7 - - - +
82A GLY* 1.3 57.2 + - - +
83A GLY 3.3 0.2 - - - -
84A ALA* 3.1 11.2 + - + +
85A PHE* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG 3.2 1.4 - - - -
81A ALA* 1.3 78.6 - - - +
83A GLY* 1.3 56.5 + - - +
85A PHE* 3.3 7.6 + - - +
86A ALA* 2.8 30.5 + - - +
157A TYR* 3.5 33.2 + - - -
179A VAL* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY* 3.1 28.3 - - - +
77A ALA* 3.7 14.4 - - - -
80A ARG 3.3 5.6 + - - -
82A GLY* 1.3 76.7 - - - +
84A ALA* 1.3 56.5 + - - +
87A ALA* 3.1 21.0 + - - +
153A GLY 3.9 6.8 - - - -
157A TYR* 3.6 20.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.7 36.6 - - + +
73A GLY 4.1 0.4 - - - -
74A GLY* 3.7 16.5 - - - +
80A ARG 3.6 4.2 + - - +
81A ALA* 3.1 15.7 + - - +
83A GLY* 1.3 74.4 - - - +
85A PHE* 1.3 58.5 + - - +
87A ALA* 3.3 4.0 + - - +
88A LEU* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 3.0 14.9 + - - +
82A GLY* 3.3 7.2 + - - +
84A ALA* 1.3 74.0 - - - +
86A ALA* 1.3 63.3 + - - +
88A LEU* 3.3 22.7 + - + +
89A LEU* 3.0 47.5 + - + +
180A PRO* 4.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 2.8 16.9 + - - +
83A GLY* 4.0 0.7 - - - +
85A PHE* 1.3 80.2 - - - +
87A ALA* 1.3 57.9 + - - +
89A LEU* 3.5 2.9 + - - -
90A ALA* 2.9 30.1 + - - +
153A GLY* 3.3 26.1 - - - +
157A TYR* 4.6 0.4 - - + -
179A VAL* 3.8 14.6 - - + -
183A VAL* 3.8 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.2 33.2 - - - +
73A GLY* 3.6 8.1 - - - -
83A GLY 3.1 19.1 + - - +
84A ALA 3.7 6.1 - - - +
85A PHE 3.2 0.2 - - - -
86A ALA* 1.3 74.6 - - - +
88A LEU* 1.3 59.5 + - - +
90A ALA* 3.4 1.6 + - - +
91A PHE* 2.8 29.5 + - - +
149A THR* 3.5 24.4 - - - +
150A GLY 4.2 0.7 - - - +
153A GLY* 3.7 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.9 31.6 - - + -
69A ALA* 5.5 0.2 - - - -
70A VAL* 4.0 16.1 - - + +
84A ALA 3.0 14.0 + - - +
85A PHE* 3.6 28.7 - - + +
87A ALA* 1.3 76.4 - - - +
89A LEU* 1.3 58.7 + - - +
91A PHE* 3.1 5.9 + - + +
92A VAL* 2.8 46.4 + - + +
134A LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.0 33.7 + - + +
86A ALA* 3.9 5.2 - - - +
88A LEU* 1.3 76.9 - - - +
90A ALA* 1.3 58.3 + - - +
92A VAL* 3.3 9.8 + - + +
93A LEU* 2.9 48.8 + - + +
180A PRO* 3.8 41.7 - - + +
183A VAL* 3.8 11.4 - - + -
184A ILE* 4.7 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 2.9 19.4 + - - +
87A ALA 3.8 3.8 - - - +
89A LEU* 1.3 75.7 - - - +
91A PHE* 1.3 57.6 + - - +
94A THR* 2.7 36.0 + - - -
149A THR* 3.7 21.5 - - - +
152A LEU* 4.2 12.3 - - + -
153A GLY 4.7 3.6 - - - +
183A VAL* 3.5 7.3 - - + +
187A SER* 3.3 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A HIS* 3.6 52.9 - + - -
66A ILE* 3.6 35.2 - - + -
69A ALA* 4.1 6.3 - - + -
87A ALA 2.8 19.1 + - - +
88A LEU* 3.1 8.7 + - - +
90A ALA* 1.3 78.0 - - - +
92A VAL* 1.3 63.6 + - - +
95A ASN* 2.6 42.9 + - - +
133A VAL* 3.9 19.5 - - + -
134A LEU* 4.2 10.1 - - + -
145A VAL* 3.9 16.2 - - + -
146A GLY* 4.2 2.0 - - - -
149A THR* 3.6 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 2.8 35.8 + - + +
89A LEU* 3.6 12.3 - - + +
91A PHE* 1.3 77.9 - - + +
93A LEU* 1.3 68.8 + - + +
95A ASN* 4.0 2.1 - - - +
96A ARG* 3.1 32.8 + - + +
134A LEU* 3.6 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 2.9 37.2 + - + +
92A VAL* 1.3 85.8 - - + +
94A THR* 1.3 61.8 + - - +
96A ARG* 4.2 9.0 - - + -
97A ILE* 2.8 48.6 + - + +
183A VAL 4.9 0.7 - - - +
184A ILE* 3.6 46.0 - - + +
187A SER* 4.0 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 2.7 22.5 + - - +
91A PHE 4.5 0.2 - - - -
93A LEU* 1.3 77.0 - - - +
95A ASN* 1.3 63.1 + - - +
98A THR* 3.2 24.6 + - - +
141A MSE 5.1 0.4 - - + -
145A VAL* 4.2 7.4 - - + -
149A THR* 3.5 21.8 - - + +
152A LEU* 4.7 0.9 - - - +
187A SER* 3.4 26.9 + - - -
190A THR* 4.2 11.5 - - + -
191A ALA* 3.6 8.9 - - + +
194A LEU* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 2.6 53.7 + - - +
92A VAL 4.1 1.8 - - - +
93A LEU 3.3 0.4 - - - -
94A THR* 1.3 76.4 - - - +
96A ARG* 1.3 63.0 + - - +
98A THR* 3.1 21.4 - - - +
99A GLY 3.5 0.2 + - - -
133A VAL* 3.7 32.5 - - + +
137A PRO 3.3 3.6 - - - +
138A ALA* 3.1 21.8 - - + +
139A LEU 4.5 1.0 - - - +
141A MSE 3.5 18.7 - - - +
145A VAL* 3.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.1 24.6 + - + +
93A LEU* 3.1 13.0 + - + +
95A ASN* 1.3 77.3 - - - +
97A ILE* 1.3 66.5 + - + +
99A GLY* 3.2 3.6 + - - -
100A ALA* 3.0 23.8 + - + +
133A VAL 6.1 0.4 - - - -
134A LEU 4.5 8.1 + - - -
135A GLY 4.9 2.4 + - - -
136A ALA* 3.4 32.6 - - - +
137A PRO 4.3 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 2.8 40.3 + - + +
96A ARG* 1.3 74.6 - - + +
98A THR* 1.3 57.1 + - - +
100A ALA* 3.0 6.9 + - + +
101A ILE* 2.8 46.8 + - + +
184A ILE* 5.0 1.6 - - + +
187A SER* 4.0 4.0 - - - +
188A THR* 3.4 48.5 - - + +
191A ALA* 3.6 17.3 - - + -
192A ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.2 14.9 + - - +
95A ASN* 3.1 17.7 - - - +
97A ILE* 1.3 77.7 - - - +
99A GLY* 1.3 56.4 + - - +
101A ILE 4.2 0.9 - - - -
102A PHE* 3.1 26.3 - - - -
130A PHE* 4.1 3.3 - - - -
139A LEU* 3.2 45.5 - - - +
141A MSE 3.8 17.0 - - + +
191A ALA* 3.9 11.8 + - - +
194A LEU* 4.6 2.9 - - - +
195A SER* 3.2 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN 3.5 0.8 + - - -
96A ARG 3.2 3.4 + - - -
97A ILE 3.1 0.4 - - - -
98A THR* 1.3 81.5 - - - +
100A ALA* 1.3 61.7 + - - +
101A ILE 3.3 0.7 - - - -
102A PHE* 3.7 1.8 + - - -
103A GLY 3.5 2.4 + - - -
104A VAL* 3.2 34.0 + - - +
130A PHE* 4.7 7.2 - - - -
137A PRO* 3.6 29.4 - - - -
138A ALA* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.0 19.2 + - + +
97A ILE* 3.0 8.0 + - + +
99A GLY* 1.3 76.3 - - - +
101A ILE* 1.3 65.9 + - - +
103A GLY* 3.2 13.6 + - - +
104A VAL 5.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 2.8 34.7 + - + +
98A THR 4.4 2.0 - - - +
100A ALA* 1.3 78.8 - - + +
102A PHE* 1.3 67.9 + - + +
103A GLY 3.4 0.5 + - - -
191A ALA 4.1 0.7 - - - +
192A ILE* 3.9 31.2 - - + -
195A SER* 3.3 36.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR 3.1 26.0 - - - -
99A GLY 3.7 2.3 + - - +
100A ALA 3.3 0.4 - - - -
101A ILE* 1.3 80.2 - - + +
103A GLY* 1.3 62.5 + - - +
104A VAL* 3.5 8.7 + - + -
108A MSE 5.5 0.2 - - - +
116A VAL* 3.6 38.4 - - + +
117A SER 3.6 15.0 - - - -
118A SER* 4.4 6.7 - - - -
124A LEU* 4.0 13.9 - - + -
130A PHE* 3.4 25.8 - + + -
139A LEU* 3.9 12.6 - - + -
195A SER* 3.4 42.4 - - - -
199A PRO* 4.0 11.4 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il