Contacts of the helix formed by residues 85 - 89 (chain L) in PDB entry 4WEB
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 GLN 85 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15L VAL* 3.8 16.6 - - - +
16L GLY* 4.7 1.9 + - - -
67L ARG* 3.5 33.2 - - - +
83L SER* 3.3 16.1 + - - +
84L VAL* 1.3 87.3 - - - +
86L ALA* 1.3 67.1 + - - +
87L GLU* 3.1 11.4 + - + +
88L ASP* 2.9 31.7 + - - +
112L ILE* 3.4 11.0 - - - +
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L VAL* 3.5 17.9 - - + +
85L GLN* 1.3 75.7 - - - +
87L GLU* 1.3 59.7 + - - +
88L ASP 3.4 1.2 + - - -
89L LEU* 3.8 14.9 + - - +
112L ILE* 3.9 10.3 - - - +
173L ASP 4.5 0.3 - - - +
174L SER* 3.3 27.2 - - - +
175L LYS* 3.9 17.3 - - - +
177L SER* 4.1 12.3 - - - +
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Residues in contact with GLU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LYS* 3.2 37.8 + - - +
67L ARG* 3.9 14.4 + - - +
85L GLN* 4.1 8.5 - - + +
86L ALA* 1.3 75.7 - - - +
88L ASP* 1.3 66.6 + - - +
89L LEU 3.2 8.4 + - - +
174L SER* 3.7 22.1 - - - +
302L ARF 3.7 16.1 - - - +
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Residues in contact with ASP 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L GLN* 4.1 1.8 - - - +
67L ARG* 2.8 35.8 + - - -
68L PHE* 3.5 10.4 - - - -
81L ILE* 3.8 6.5 - - + +
84L VAL* 3.8 15.3 - - + +
85L GLN* 2.9 30.0 + - - +
87L GLU* 1.3 77.0 - - - +
89L LEU* 1.3 65.0 + - - +
90L ALA* 3.3 2.9 + - - +
92L TYR* 2.8 29.3 + - - +
110L LEU* 3.3 9.0 - - + +
302L ARF 2.7 27.8 - - - +
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LYS* 3.7 15.1 - - - +
46L PRO* 3.8 23.8 - - + +
85L GLN 4.3 1.2 + - - -
86L ALA 3.8 13.0 + - - +
87L GLU 3.2 3.6 - - - +
88L ASP* 1.3 77.9 - - - +
90L ALA* 1.3 62.6 + - - +
110L LEU* 3.6 19.0 - - - +
111L GLU* 6.2 1.3 - - + -
112L ILE* 4.1 15.1 - - + +
171L ASP* 5.2 0.9 - - + -
172L GLN* 3.2 55.4 - - + +
173L ASP 3.4 21.3 - - - +
174L SER* 3.9 7.0 - - - -
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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