Contacts of the helix formed by residues 87 - 101 (chain E) in PDB entry 3X0X
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 87 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E TRP* 4.9 1.6 - - + -
35E ALA* 5.0 3.3 - - - +
38E ARG* 2.6 40.1 + - - +
83E ILE 3.1 7.7 + - - +
84E ALA* 3.3 5.9 + - - +
86E ALA* 1.3 85.2 - - + +
88E GLY* 1.3 64.5 + - - +
89E SER* 3.1 14.7 + - - -
90E LEU* 2.9 45.4 + - + +
91E GLY 3.0 17.5 + - - -
212E GLN* 4.4 0.3 - - - +
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Residues in contact with GLY 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ALA* 3.4 14.4 + - - -
87E ASP* 1.3 70.7 + - - +
89E SER* 1.3 57.0 + - - +
91E GLY* 3.4 0.9 + - - -
92E HIS* 2.8 30.8 + - - +
210E MET* 3.6 11.3 - - - +
261E VAL* 4.0 2.1 - - - +
265E ILE* 3.7 24.2 - - - +
384E ASN* 3.9 16.0 - - - +
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Residues in contact with SER 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ASP* 3.1 11.2 + - - -
88E GLY* 1.3 74.0 - - - +
90E LEU* 1.3 57.0 + - - +
92E HIS* 3.2 3.5 + - - +
93E LEU* 2.7 36.5 + - - +
210E MET* 3.3 20.4 - - - -
211E ARG 3.5 1.2 + - - -
212E GLN* 3.0 48.1 + - - +
213E THR* 3.7 9.1 - - - +
384E ASN* 4.4 4.7 + - - +
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Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E TRP* 3.3 45.5 - - + -
38E ARG* 4.2 1.8 - - - +
45E ALA* 3.7 28.9 - - + +
48E GLU* 3.8 20.9 - - + -
49E ARG* 5.2 1.3 - - + +
52E LEU* 5.0 7.4 - - + +
83E ILE* 3.7 15.5 - - + -
87E ASP* 2.9 35.0 + - + +
89E SER* 1.3 74.8 - - - +
91E GLY* 1.3 54.1 + - - +
93E LEU* 3.7 15.8 - - + +
94E PHE* 2.7 38.3 + - - +
212E GLN 5.3 0.2 - - - +
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Residues in contact with GLY 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E VAL* 4.3 5.4 - - - +
83E ILE* 3.6 15.1 - - - +
84E ALA* 3.9 17.0 - - - -
87E ASP 3.0 13.2 + - - -
88E GLY 3.7 3.6 - - - -
90E LEU* 1.3 75.4 - - - +
92E HIS* 1.3 56.7 + - - +
94E PHE* 4.1 1.0 - - - +
95E GLY* 2.8 30.0 + - - -
261E VAL* 3.7 10.8 - - - +
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Residues in contact with HIS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLY 2.8 19.9 + - - +
89E SER 3.6 3.4 - - - +
91E GLY* 1.3 73.9 - - - +
93E LEU* 1.3 65.0 + - - +
96E TYR* 3.0 55.6 + + + +
163E SER* 4.3 10.5 - - - -
210E MET* 4.1 11.4 - - + -
213E THR* 3.5 30.6 + - + +
215E SER* 4.7 5.2 - - - -
258E PHE* 4.3 10.3 - + - -
261E VAL* 3.9 14.1 - - + +
388E HIS* 3.1 45.7 + + - -
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E ALA* 5.4 1.1 - - + -
49E ARG* 3.6 51.4 - - + +
89E SER 2.7 19.1 + - - +
90E LEU* 3.7 15.7 - - + +
92E HIS* 1.3 76.9 + - - +
94E PHE* 1.3 61.6 + - - +
96E TYR* 4.1 3.4 - - - +
97E HIS* 3.0 24.3 + - - +
126E TRP* 3.9 15.5 - - + -
163E SER 5.2 0.4 - - - -
164E GLY* 3.8 16.6 - - - +
212E GLN 3.8 18.8 - - - +
213E THR* 3.5 25.8 - - - +
214E ASP* 4.3 0.4 - - - +
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Residues in contact with PHE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LEU* 4.0 28.0 - - + -
57E LEU* 3.6 45.3 - - + -
58E LEU* 4.1 19.5 - - + -
60E LEU* 4.2 5.6 - - + -
79E VAL* 3.7 20.6 - - + -
80E VAL* 4.1 13.7 - - + -
83E ILE* 3.9 18.2 - - + -
90E LEU 2.7 21.6 + - - +
91E GLY* 4.1 2.0 - - - +
93E LEU* 1.3 72.6 - - - +
95E GLY* 1.3 64.3 + - - +
97E HIS* 3.3 8.5 + + - +
98E LEU* 3.0 53.3 + - + +
126E TRP* 4.4 3.5 - - - -
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Residues in contact with GLY 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E VAL* 4.1 15.9 - - - -
91E GLY 2.8 22.6 + - - -
92E HIS* 3.9 0.4 - - - -
94E PHE* 1.3 73.5 - - - +
96E TYR* 1.3 60.9 + - - +
98E LEU* 3.1 19.0 + - - +
99E THR* 3.4 11.1 + - - +
257E ILE* 3.6 25.7 - - - +
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Residues in contact with TYR 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E HIS* 3.0 41.0 + + + +
93E LEU* 4.1 2.5 - - - +
95E GLY* 1.3 71.4 - - - +
97E HIS* 1.3 67.0 + - - +
98E LEU 3.0 1.6 - - - -
99E THR* 2.5 48.0 + - + -
100E ASN* 3.5 7.6 - - - -
129E ASN* 3.4 23.7 + - - +
131E SER* 5.2 4.6 + - - -
132E SER* 5.6 1.4 + - - -
163E SER* 3.2 34.0 + - - +
250E PHE* 5.6 9.9 - + - -
254E ALA* 5.2 5.5 - - + +
257E ILE* 4.3 2.7 - - - +
258E PHE* 3.7 27.0 - + - -
388E HIS* 4.8 2.7 - - - -
391E HIS* 3.7 21.5 + + - -
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Residues in contact with HIS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU* 2.8 47.8 + - + -
93E LEU 3.0 16.6 + - - +
94E PHE* 3.4 11.4 - + - +
96E TYR* 1.3 73.6 - - - +
98E LEU* 1.3 78.1 + - + +
100E ASN* 3.1 22.2 + - - +
101E ALA* 4.2 3.0 + - + -
120E ILE* 5.1 3.1 - - + -
125E TRP 3.5 23.8 - - - -
126E TRP* 3.7 17.6 - + + -
127E THR* 3.1 50.1 + - + +
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Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU 4.6 2.9 - - - +
60E LEU* 4.2 15.5 - - + -
61E LEU* 4.1 26.1 - - + +
73E TRP* 4.6 0.6 - - - -
76E ALA* 4.1 23.6 - - + +
80E VAL* 3.9 19.3 - - + -
94E PHE* 3.0 51.5 + - + +
95E GLY 3.2 9.9 - - - +
96E TYR 3.0 0.4 - - - -
97E HIS* 1.3 92.7 - - + +
99E THR* 1.3 54.8 + - - +
102E PRO* 3.2 26.2 - - - +
257E ILE* 4.4 9.2 - - + -
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Residues in contact with THR 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TRP* 5.3 0.2 - - - -
95E GLY 3.6 7.2 - - - +
96E TYR* 2.5 41.8 + - + +
98E LEU* 1.3 75.9 - - - +
100E ASN* 1.3 68.1 + - - +
102E PRO* 3.9 12.1 - - - +
103E MET 4.2 2.6 + - - -
250E PHE* 4.3 22.1 - - - -
253E ILE* 4.2 14.9 - - + +
254E ALA* 4.0 22.7 - - + -
257E ILE* 3.4 28.5 - - + -
258E PHE* 5.8 0.7 - - + -
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Residues in contact with ASN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E TYR 3.5 15.0 + - - +
97E HIS* 3.1 7.0 + - - +
98E LEU 3.2 0.2 - - - -
99E THR* 1.3 78.7 + - - +
101E ALA* 1.3 69.6 + - - +
103E MET* 3.0 33.7 + - - +
127E THR* 2.7 48.4 + - - +
128E GLY* 3.5 14.7 - - - +
129E ASN* 3.1 27.8 + - - +
163E SER 5.2 0.4 + - - -
172E PHE* 3.8 18.7 - - + -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E VAL* 5.2 5.4 - - + -
97E HIS* 4.2 4.3 + - + +
100E ASN* 1.3 76.4 - - - +
102E PRO* 1.4 60.9 - - + +
104E ILE* 2.8 48.7 + - + +
117E TYR* 3.5 24.5 + - + -
120E ILE* 3.7 25.4 - - + -
127E THR* 4.4 2.8 + - + -
172E PHE* 4.0 3.7 - - - -
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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
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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