Contacts of the helix formed by residues 81 - 99 (chain A) in PDB entry 4WPN
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 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR 4.8 2.4 - - - +
80A MET* 1.3 79.5 - - - +
82A ALA* 1.3 65.5 + - - +
83A SER* 3.6 19.7 + - - +
84A GLU* 3.0 20.7 + - + +
85A ARG* 3.2 9.2 + - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET 3.4 2.4 + - - -
81A ASP* 1.3 72.0 - - - +
83A SER* 1.3 63.1 + - - +
85A ARG* 3.1 28.8 + - - +
86A GLY 3.1 16.8 + - - -
137A ALA* 3.4 32.6 - - - +
138A ASP* 3.7 11.9 - - + -
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 3.6 15.9 + - - +
82A ALA* 1.3 78.8 - - - +
84A GLU* 1.3 57.6 + - - +
86A GLY* 3.3 3.3 + - - +
87A ARG* 2.9 25.5 + - - +
137A ALA* 5.3 0.2 - - - -
138A ASP* 3.4 30.3 - - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A MET* 3.6 25.7 - - + +
81A ASP* 3.0 22.4 + - + +
83A SER* 1.3 77.6 + - - +
85A ARG* 1.3 64.4 + - - +
86A GLY 3.1 0.9 - - - -
87A ARG* 3.3 18.1 + - - +
88A LEU* 3.0 35.1 + - + +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A TRP* 3.7 43.4 + - + -
78A ARG 5.8 1.8 + - - -
80A MET* 3.8 19.5 + - + -
81A ASP 3.2 9.4 + - - +
82A ALA* 3.1 28.6 + - - +
84A GLU* 1.3 75.8 - - - +
86A GLY* 1.3 63.6 + - - +
88A LEU* 3.3 4.2 + - - +
89A LEU* 3.1 28.9 + - - +
137A ALA* 3.4 21.2 + - + -
140A ILE* 5.2 3.4 - - - +
184A LEU 3.5 16.9 + - - +
185A SER* 2.8 26.6 + - - -
186A CYS* 3.8 10.5 + - - +
187A GLY* 3.6 15.9 - - - +
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Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 3.1 10.1 + - - -
83A SER* 3.3 5.8 + - - -
84A GLU 3.1 0.2 - - - -
85A ARG* 1.3 77.4 - - - +
87A ARG* 1.3 56.9 + - - +
89A LEU* 3.2 1.8 + - - -
90A TYR* 2.9 39.1 + - - -
134A ALA* 3.3 29.6 - - - +
137A ALA* 3.7 8.4 - - - +
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER 2.9 14.5 + - - +
84A GLU* 3.4 26.5 - - - +
86A GLY* 1.3 75.7 - - - +
88A LEU* 1.3 57.3 + - + +
90A TYR* 3.3 29.5 + - - +
91A LYS* 2.9 37.9 + - + +
94A ASP* 5.3 5.3 + - - -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 3.9 25.6 - - + -
80A MET* 3.9 18.6 - - + -
84A GLU* 3.0 29.4 + - + +
85A ARG 3.7 6.1 - - - +
86A GLY 3.3 0.2 - - - -
87A ARG* 1.3 75.4 - - - +
89A LEU* 1.3 57.4 + - - +
91A LYS* 3.3 6.4 + - + +
92A LEU* 2.9 28.4 + - - +
212A ALA* 3.3 28.1 - - - +
213A GLY 3.6 23.6 - - - +
214A PHE* 3.6 25.8 - - + +
215A PRO* 4.4 1.6 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TRP* 5.8 0.2 - - + -
85A ARG* 3.1 17.7 + - + +
86A GLY* 3.2 7.1 + - - +
88A LEU* 1.3 74.9 - - - +
90A TYR* 1.3 59.0 + - - +
92A LEU* 3.4 6.7 + - + +
93A ALA* 3.0 25.6 + - - +
130A LEU* 3.8 29.5 - - + +
133A CYS* 4.6 0.7 - - + -
134A ALA* 3.6 24.5 - - + +
180A ILE* 5.9 0.2 - - + -
181A GLY* 4.0 7.2 - - - +
184A LEU* 4.0 23.8 - - + -
185A SER* 3.7 39.3 - - - +
214A PHE* 3.9 19.1 - - + -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLY* 2.9 30.5 + - - -
87A ARG* 3.6 24.2 - - - +
89A LEU* 1.3 72.1 - - - +
91A LYS* 1.3 66.3 + - - +
93A ALA* 3.2 7.5 + - - +
94A ASP* 3.0 30.2 + - - +
131A ARG* 3.4 38.0 + - + +
134A ALA* 3.5 22.2 - - + -
135A GLY* 3.2 22.1 - - - -
139A LYS* 5.6 0.2 + - - -
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Residues in contact with LYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 2.9 26.9 + - + +
88A LEU* 3.5 8.3 - - + +
90A TYR* 1.3 77.6 - - - +
92A LEU* 1.3 62.4 + - - +
94A ASP* 3.2 16.0 + - + +
95A LEU* 3.0 45.8 + - + +
211A GLU* 5.5 3.4 - - - -
212A ALA* 4.0 25.8 - - + +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU 2.9 14.8 + - - +
89A LEU* 3.6 10.1 - - + +
91A LYS* 1.3 76.4 - - - +
93A ALA* 1.3 64.0 + - - +
95A LEU* 3.2 3.3 + - - +
96A ILE* 3.0 27.2 + - + +
130A LEU* 3.7 21.3 - - + -
177A ILE* 5.9 0.7 - - + -
180A ILE* 4.5 13.9 - - + -
184A LEU* 5.7 0.7 - - + -
205A VAL* 4.4 9.9 - - + +
208A LEU* 3.7 40.8 - - + +
209A ILE* 3.8 27.4 - - + +
212A ALA* 4.3 4.7 - - - +
214A PHE* 4.1 15.7 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU 3.0 13.8 + - - +
90A TYR 3.2 8.9 + - - +
92A LEU* 1.3 76.6 - - - +
94A ASP* 1.3 56.4 + - - +
96A ILE* 3.3 6.3 + - - +
97A GLU* 2.9 28.8 + - - +
127A ILE* 4.1 11.8 - - + +
130A LEU* 3.4 23.0 - - + +
131A ARG* 3.8 33.0 - - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 5.3 5.0 + - - -
90A TYR* 3.0 22.1 + - - +
91A LYS* 3.2 21.7 + - + +
93A ALA* 1.3 75.6 - - - +
95A LEU* 1.3 59.2 + - + +
97A GLU* 3.4 7.4 + - - +
98A ARG* 2.9 27.0 + - - +
131A ARG* 2.8 34.1 + - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 3.0 32.4 + - - +
92A LEU* 3.6 8.1 - - - +
93A ALA 3.2 0.4 - - - -
94A ASP* 1.3 77.6 - - + +
96A ILE* 1.3 59.4 + - - +
98A ARG* 3.2 38.3 + - + +
99A ASP* 2.9 31.0 + - - +
208A LEU* 3.5 39.5 - - + +
211A GLU* 3.8 18.4 - - + +
212A ALA* 3.9 23.8 - - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 3.0 24.3 + - + +
93A ALA 3.7 6.5 - - - +
95A LEU* 1.3 73.6 - - - +
97A GLU* 1.3 61.3 + - - +
99A ASP 3.2 3.1 + - - -
100A ARG* 3.0 26.7 + - - +
103A LEU* 3.8 12.1 - - + -
123A LEU* 3.6 26.4 - - + +
126A CYS* 4.9 8.3 - - + +
127A ILE* 4.0 11.9 - - + -
130A LEU* 3.9 22.2 - - + -
173A LEU* 5.5 2.2 - - + -
177A ILE* 4.3 20.0 - - + -
205A VAL* 4.6 11.2 - - + -
208A LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA 2.9 13.8 + - - +
94A ASP* 3.4 11.8 - - - +
96A ILE* 1.3 76.9 - - - +
98A ARG* 1.3 62.1 + - - +
100A ARG* 3.2 25.8 + - - +
127A ILE* 3.8 23.0 - - + +
131A ARG* 2.9 38.3 + - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ASP 2.9 14.8 + - - +
95A LEU* 3.2 24.1 + - + +
97A GLU* 1.3 76.5 - - - +
99A ASP* 1.3 88.3 + - - +
100A ARG 3.4 2.6 + - - -
101A LEU* 5.0 1.0 + - - +
208A LEU* 3.5 8.7 - - - +
211A GLU* 2.8 41.8 + - - -
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU 2.9 17.1 + - - +
96A ILE 3.2 5.3 + - - +
98A ARG* 1.3 105.6 + - - +
100A ARG* 1.3 62.7 + - - +
101A LEU 3.4 2.7 - - - -
102A LEU* 3.3 17.4 + - + +
103A LEU* 2.9 29.3 + - + +
204A HIS* 2.7 36.3 + - - +
208A LEU* 3.4 15.3 - - + +
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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
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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) + - + + + + + -
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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