Contacts of the helix formed by residues 78 - 97 (chain A) in PDB entry 2FX0
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 ASN 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.1 17.3 + - - +
76A GLN 3.2 2.3 + - - +
77A PHE* 1.3 74.9 - - - +
79A PRO* 1.3 63.9 - - - +
80A ILE* 3.1 17.3 + - - +
81A ASN* 3.0 45.0 + - + +
82A ALA* 2.9 31.3 + - - +
139A GLN* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.2 10.8 - - + -
77A PHE 3.3 7.2 - - - +
78A ASN* 1.3 85.8 - - - +
80A ILE* 1.3 67.2 + - + +
82A ALA* 4.3 0.9 - - + -
83A LEU* 3.0 29.7 + - - +
132A ILE* 3.5 11.4 - - + +
135A GLU* 4.2 3.4 - - + -
136A GLY* 3.5 38.1 - - - +
139A GLN* 3.4 30.1 - - - +
141A VAL* 4.2 6.5 - - + -
142A PHE* 3.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.1 15.1 + - - +
79A PRO* 1.3 81.4 - - + +
81A ASN* 1.3 60.5 + - - +
83A LEU* 3.3 2.2 + - - +
84A ARG* 2.8 61.6 + - - +
141A VAL* 3.6 36.8 - - + -
142A PHE* 4.2 16.4 - - + -
192A ILE* 4.1 16.1 - - + +
196A THR* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 3.4 24.6 + - + +
78A ASN* 3.0 33.3 + - - +
80A ILE* 1.3 79.0 - - - +
82A ALA* 1.3 65.8 + - - +
84A ARG* 3.4 11.5 + - - +
85A GLU* 2.9 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.5 28.3 - - - +
72A LEU* 3.8 19.7 - - + +
75A ASN* 3.5 13.1 - - - +
78A ASN 2.9 19.6 + - - +
79A PRO 4.1 2.5 - - - +
81A ASN* 1.3 75.3 - - - +
83A LEU* 1.3 56.8 + - - +
85A GLU* 3.2 3.5 + - - +
86A TYR* 2.9 29.3 + - - +
132A ILE* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO 3.0 20.7 + - - +
80A ILE 3.8 2.7 - - - +
82A ALA* 1.3 73.6 - - - +
84A ARG* 1.3 60.3 + - - +
86A TYR* 4.2 6.7 - - + -
87A LEU* 2.9 60.0 + - + +
129A LEU* 3.8 29.4 - - + -
132A ILE* 3.6 15.8 - - + +
133A LEU* 4.4 3.6 - - + -
142A PHE* 3.7 13.2 - - + -
154A ILE* 5.5 1.3 - - + -
191A ILE* 4.7 0.9 - - + -
192A ILE* 3.7 17.9 - - + -
195A LEU* 3.5 32.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
80A ILE* 2.8 33.7 + - - +
81A ASN* 3.6 11.7 - - - +
83A LEU* 1.3 72.3 - - - +
85A GLU* 1.3 57.0 + - - +
88A THR* 2.9 35.1 + - - +
188A VAL* 3.9 18.7 - - + +
189A SER* 2.8 31.0 + - - -
192A ILE* 3.5 40.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 4.7 1.0 - - - +
71A PHE* 3.3 25.6 - - + -
74A LYS* 2.7 43.4 + - - +
75A ASN* 3.0 24.3 + - - +
81A ASN 2.9 17.0 + - - +
82A ALA 3.6 3.6 - - - +
84A ARG* 1.3 75.9 - - - +
86A TYR* 1.3 57.8 + - - +
88A THR* 3.4 6.3 + - + -
89A VAL* 2.9 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 5.0 0.9 - - + -
71A PHE* 3.7 33.3 - + + -
82A ALA 2.9 17.5 + - - +
83A LEU* 3.3 5.4 + - + +
85A GLU* 1.3 78.2 - - - +
87A LEU* 1.3 75.4 - - + +
89A VAL* 3.4 1.4 + - - +
90A PHE* 3.0 62.5 + + + -
125A SER* 2.7 32.1 + - - -
126A PHE* 4.8 0.7 - - - -
128A GLN* 4.2 6.1 - - + -
129A LEU* 3.4 39.6 - - + +
132A ILE* 3.9 19.3 - - + -
154A ILE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 2.9 41.8 + - + +
86A TYR* 1.3 88.7 - - + +
88A THR* 1.3 54.5 + - - +
90A PHE* 3.9 2.6 - - + +
91A THR* 2.8 45.1 + - + +
129A LEU* 5.0 0.2 - - + -
154A ILE* 4.0 26.0 - - + -
158A VAL* 4.5 9.6 - - + -
188A VAL* 4.0 31.0 - - + +
191A ILE* 3.8 39.7 - - + -
192A ILE* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.9 22.3 + - - +
85A GLU* 3.7 6.7 - - + +
87A LEU* 1.3 74.7 - - - +
89A VAL* 1.3 68.6 + - + +
91A THR* 3.8 5.4 - - - -
92A THR* 2.9 41.0 + - + +
188A VAL* 4.0 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.0 12.3 - - + -
68A LEU* 4.0 26.7 - - + -
69A PRO* 6.0 0.9 - - + -
71A PHE* 3.9 20.9 - - + -
85A GLU* 2.9 27.8 + - + +
86A TYR 3.7 5.2 - - - +
88A THR* 1.3 75.7 - - + +
90A PHE* 1.3 65.4 + - + +
92A THR* 3.2 14.5 + - - -
93A HIS* 3.4 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.3 20.6 - - + -
68A LEU* 3.9 15.9 - - + -
71A PHE* 5.4 0.4 - + - -
86A TYR* 3.0 62.5 + + + +
87A LEU* 3.9 4.7 - - + +
89A VAL* 1.3 80.0 - - + +
91A THR* 1.3 60.0 + - - +
93A HIS* 3.3 4.9 + - - +
94A ILE* 2.9 59.3 + - + +
100A ILE* 4.9 11.9 - - + -
125A SER* 3.1 34.5 - - - -
158A VAL* 4.4 9.6 - - + -
159A LEU* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 2.8 31.3 + - + +
88A THR* 3.4 8.1 + - - -
90A PHE* 1.3 72.9 - - - +
92A THR* 1.3 66.1 + - - +
94A ILE* 4.2 3.2 - - - +
95A LYS* 3.2 25.6 + - - +
158A VAL* 3.8 28.9 - - + +
187A LEU* 4.2 24.0 - - + -
188A VAL* 4.6 10.7 - - + +
191A ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 2.9 34.2 + - + +
89A VAL* 3.2 7.6 + - - -
91A THR* 1.3 80.3 + - - +
93A HIS* 1.3 69.2 + - - +
95A LYS* 3.4 12.4 - - - +
96A GLU* 3.2 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A TYR 4.5 13.7 + - - -
64A LEU* 3.5 46.1 - - + +
89A VAL* 3.4 15.7 + - + +
90A PHE* 3.3 4.4 + - - +
92A THR* 1.3 82.2 + - - +
94A ILE* 1.3 62.5 + - - +
96A GLU* 4.6 2.9 - - - -
97A ASN* 2.9 57.9 + - + +
100A ILE* 5.3 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 2.9 44.8 + - + +
91A THR 4.2 3.1 - - - +
93A HIS* 1.3 76.9 - - - +
95A LYS* 1.3 65.9 + - - +
97A ASN 3.2 17.5 - - - -
98A PRO* 3.3 8.7 - - + +
100A ILE* 3.7 32.1 - - + -
101A GLY* 5.5 2.0 - - - +
158A VAL* 3.8 31.6 - - + +
159A LEU* 3.8 39.3 - - + +
161A PRO* 5.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR 3.2 16.7 + - - +
92A THR* 3.4 16.8 - - - +
94A ILE* 1.3 79.7 - - - +
96A GLU* 1.3 89.0 + - - +
97A ASN 3.4 0.2 + - - -
98A PRO* 3.5 13.7 - - - +
161A PRO* 6.2 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.2 20.5 + - - +
93A HIS* 4.0 4.3 - - - +
95A LYS* 1.3 108.3 + - + +
97A ASN* 1.3 74.7 + - - +
98A PRO* 3.6 5.2 - - - +
99A GLU* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.1 25.4 + - - +
93A HIS* 2.9 49.0 + - + +
94A ILE 3.2 4.2 - - - +
96A GLU* 1.3 91.1 - - - +
98A PRO* 1.4 52.4 - - - +
99A GLU* 2.8 28.7 + - - +
100A ILE* 3.2 22.7 + - + +
----------------------------------------------------------
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