Contacts of the helix formed by residues 74 - 92 (chain A) in PDB entry 3FIW
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 ASP 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLY 3.8 1.4 + - - -
73A GLU* 1.3 72.9 - - - +
75A TRP* 1.3 66.5 + - - +
76A HIS* 3.2 19.5 + - - +
77A GLY* 3.0 24.6 + - - +
78A TRP* 3.1 23.0 + - - +
81A ARG* 4.9 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 3.1 4.4 + - - -
74A ASP* 1.3 75.5 + - - +
76A HIS* 1.3 73.8 + + + +
78A TRP* 3.8 4.1 - - - +
79A PHE* 3.0 32.7 + + + +
118A PHE* 3.5 19.3 - - + -
119A LEU* 3.6 17.3 - - + -
122A SER* 3.5 44.6 - - - +
124A VAL* 3.7 9.6 - - + -
180B THR* 4.5 5.6 - - + -
183B LEU* 3.6 36.3 - - + -
184B VAL* 3.9 28.7 - - + -
187B VAL* 3.6 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 3.0 14.5 - - - +
75A TRP* 1.3 98.9 - + + +
77A GLY* 1.3 62.8 + - - +
79A PHE* 3.3 5.0 + - - +
80A LEU* 3.3 35.0 + - + +
180B THR* 3.5 24.0 - - + +
181B ASP* 4.4 10.8 + - - -
184B VAL* 3.3 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASP* 3.0 21.8 + - - -
76A HIS* 1.3 73.0 + - - +
78A TRP* 1.3 59.1 + - - +
80A LEU* 3.5 11.2 + - - +
81A ARG* 2.9 39.6 + - - +
84A ARG* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 4.6 7.4 + - - -
69A PRO* 3.5 37.7 - - + +
73A GLU* 3.9 11.2 - - - +
74A ASP 3.1 18.5 + - - +
75A TRP 3.8 4.3 - - - +
77A GLY* 1.3 71.3 - - - +
79A PHE* 1.3 85.8 + + + +
81A ARG* 3.0 27.0 + - + +
82A ASN* 2.7 60.7 + - + +
115A LYS* 3.4 47.9 - - + +
118A PHE* 4.0 17.0 - + + -
119A LEU* 4.0 25.1 - - + -
133A MSE 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.0 30.6 + + + +
76A HIS 3.5 6.1 - - - +
77A GLY 3.3 0.2 - - - -
78A TRP* 1.3 88.3 - + + +
80A LEU* 1.3 64.5 + - - +
82A ASN* 3.4 2.8 + - - +
83A THR* 3.2 36.2 + - - -
119A LEU* 4.3 15.5 - - + -
132A ALA* 3.8 40.8 - - + -
133A MSE 3.7 31.9 - - + -
136A ALA* 3.9 12.3 - - + -
176B LEU* 4.3 3.6 - - + -
179B ILE* 4.8 3.8 - - + -
180B THR* 3.4 33.7 - - + -
183B LEU* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.3 31.1 + - + +
77A GLY* 3.7 9.9 - - - +
79A PHE* 1.3 78.2 - - - +
81A ARG* 1.3 57.9 + - - +
83A THR* 3.3 2.4 + - - -
84A ARG* 2.9 65.9 + - - +
173B GLU* 5.9 0.2 - - - +
176B LEU* 3.6 25.0 - - + +
177B ALA* 5.0 4.5 - - + +
180B THR* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 5.3 10.3 - - - +
73A GLU* 3.0 25.9 + - - +
74A ASP* 4.9 3.2 + - - +
77A GLY* 2.9 19.8 + - - +
78A TRP* 3.4 39.8 - - + +
80A LEU* 1.3 76.7 - - - +
82A ASN* 1.3 51.2 + - - +
84A ARG* 3.4 16.0 + - + +
85A SER* 2.8 35.8 + - - -
88A ARG* 5.2 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS* 3.3 18.4 + - - -
78A TRP* 2.7 47.3 + - + +
79A PHE* 3.6 4.9 + - + +
81A ARG* 1.3 72.0 - - - +
83A THR* 1.3 62.8 + - - +
85A SER* 3.3 4.6 + - - -
86A PHE* 3.0 23.7 + - - +
115A LYS* 3.1 30.4 + - - +
133A MSE 4.2 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE* 3.2 15.4 + - - -
80A LEU 3.8 3.6 - - - -
82A ASN* 1.3 79.5 + - - +
84A ARG* 1.3 60.9 + - - +
86A PHE* 3.2 7.1 + - + +
87A ARG* 3.0 28.8 + - - +
136A ALA* 3.7 27.2 - - + +
139A PHE* 5.4 0.9 - - + -
140A THR* 3.1 27.1 - - - +
172B PHE* 3.7 13.7 - - + -
176B LEU* 3.7 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 4.9 2.2 + - - -
80A LEU* 2.9 59.8 + - - +
81A ARG* 3.6 12.5 - - + +
83A THR* 1.3 75.6 - - - +
85A SER* 1.3 62.6 + - - +
87A ARG* 3.6 2.2 + - - +
88A ARG* 3.0 39.7 + - - +
172B PHE* 4.0 15.9 - - + -
173B GLU* 2.9 42.8 + - - +
176B LEU* 4.4 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PRO 4.6 0.5 + - - -
63A HIS* 2.9 26.2 - - - -
66A GLU* 3.3 27.5 - - - +
81A ARG 2.8 17.9 + - - -
82A ASN* 3.4 9.0 - - - -
83A THR 3.2 0.2 - - - -
84A ARG* 1.3 74.1 - - - +
86A PHE* 1.3 57.9 + - - +
88A ARG* 3.3 23.0 + - - +
89A THR* 2.8 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 4.0 15.9 - - - -
63A HIS* 3.5 27.1 - + + +
82A ASN* 3.0 14.5 + - - +
83A THR* 3.2 11.2 + - + +
85A SER* 1.3 74.7 - - - +
87A ARG* 1.3 61.8 + - - +
89A THR* 3.2 4.8 + - - -
90A LEU* 3.1 46.7 + - + +
100A HIS* 3.7 35.2 - + - -
137A GLY* 3.7 31.0 - - - -
140A THR* 3.8 19.5 - - + -
141A VAL* 4.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR 3.0 16.3 + - - +
84A ARG* 3.7 5.2 - - - +
86A PHE* 1.3 72.9 - - - +
88A ARG* 1.3 66.6 + - - +
90A LEU* 3.0 3.8 + - - +
91A LEU* 3.0 36.3 + - + +
140A THR* 3.6 15.7 - - + +
143A CYS* 5.4 1.8 - - - +
144A VAL* 3.7 19.1 - - + +
147A GLU* 2.9 34.1 + - - -
168B HIS 4.2 0.8 - - - -
169B GLU* 3.5 51.3 + - - +
172B PHE* 3.3 48.2 - - + +
3C LYS* 4.8 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 4.3 14.3 + - - -
81A ARG* 5.2 4.9 + - - +
84A ARG* 3.0 34.9 + - - +
85A SER* 3.4 34.3 + - - +
87A ARG* 1.3 76.1 - - - +
89A THR* 1.3 62.7 + - - +
91A LEU* 3.3 10.5 + - - +
92A ALA* 3.1 24.5 + - + +
3C LYS* 6.2 4.4 - - - +
5C ASN* 5.7 7.0 - - - +
7C GLU* 4.9 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 3.0 31.5 - - - +
60A MSE 3.6 18.5 - - + +
62A PRO* 4.0 11.5 - - + +
63A HIS* 3.3 38.9 + - + +
85A SER* 2.8 18.3 + - - -
86A PHE* 3.5 6.1 - - - -
87A ARG 3.1 0.2 - - - -
88A ARG* 1.3 77.2 - - - +
90A LEU* 1.3 62.2 + - - +
92A ALA* 3.2 20.2 + - - +
93A ARG* 4.3 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MSE 3.5 26.7 - - + -
86A PHE* 3.1 43.5 + - + +
87A ARG 3.0 6.9 + - - +
89A THR* 1.3 76.6 - - - +
91A LEU* 1.3 60.7 + - - +
92A ALA 3.3 1.0 + - - -
93A ARG* 3.3 3.1 + - - +
96A GLY* 3.2 33.4 - - - +
97A ALA* 4.3 13.7 - - + +
100A HIS* 3.7 29.2 - - + +
140A THR* 4.3 8.1 - - + -
141A VAL* 4.1 20.0 - - + -
144A VAL* 4.0 14.4 - - + -
148A GLN* 3.3 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.0 56.8 + - + +
88A ARG* 3.8 7.0 - - - +
90A LEU* 1.3 76.5 - - - +
92A ALA* 1.3 61.4 + - - +
93A ARG 3.2 7.0 + - - +
94A ARG* 5.5 0.2 - - - -
144A VAL* 3.8 22.2 - - + -
147A GLU* 3.7 26.2 - - + +
148A GLN* 3.5 20.1 - - + +
3C LYS* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASP* 4.2 4.7 - - - +
62A PRO* 5.6 9.2 - - + -
88A ARG* 3.1 13.3 + - + +
89A THR* 3.2 20.0 + - + +
91A LEU* 1.3 78.4 - - - +
93A ARG* 1.3 71.3 + - + +
----------------------------------------------------------
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