Contacts of the strand formed by residues 54 - 58 (chain B) in PDB entry 4AEJ
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 GLY 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B LYS 3.3 3.0 + - - -
53B SER* 1.3 75.3 - - - +
55B GLU* 1.3 61.5 + - - -
56B TYR* 3.2 13.1 - - - -
72B PHE* 3.4 18.9 - - - -
73B CYS 2.7 37.3 + - - -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLY* 1.3 71.8 - - - -
56B TYR* 1.3 75.6 + - - +
57B TRP* 5.3 4.5 + - + +
70B LYS* 3.2 47.1 + - + +
71B VAL 3.2 9.4 - - - +
72B PHE* 4.5 1.5 - - + +
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP 4.0 7.0 - - - -
32B GLY* 3.4 16.4 - - - +
44B LEU* 3.6 17.7 - - + -
51B LEU* 3.4 35.4 - - + +
52B LYS* 2.7 31.3 + - - +
54B GLY* 3.2 24.5 - - - -
55B GLU* 1.3 77.7 - - - +
57B TRP* 1.3 68.6 + - - +
58B VAL* 5.0 0.9 - - + -
70B LYS* 3.6 3.5 - - - +
71B VAL* 2.8 36.6 + - - +
73B CYS* 3.7 25.8 - - + -
75B MSE 3.7 14.4 - - + -
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Residues in contact with TRP 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLY* 2.9 13.5 + - - -
33B SER* 3.7 16.8 - - - +
34B ARG* 3.5 77.0 - - + +
37B PRO* 3.3 9.8 - - + +
38B ALA 3.2 19.2 + - - -
55B GLU* 5.3 4.3 + - + +
56B TYR* 1.3 79.4 - - - +
58B VAL* 1.3 64.2 + - - +
68B ALA* 3.7 26.0 - - + -
69B ILE 3.3 13.5 - - - -
70B LYS* 3.8 30.9 - - + +
121B ASN* 3.3 30.7 - - - -
123B GLU* 4.5 1.8 - - - -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO* 4.0 2.2 - - - -
38B ALA* 3.0 12.1 - - + +
39B ARG 3.8 7.4 - - - +
40B ASN* 3.7 26.0 - - - +
41B CYS* 4.0 5.4 - - - +
44B LEU* 5.6 1.1 - - + -
56B TYR* 5.0 1.1 - - + -
57B TRP* 1.3 80.6 - - - +
59B ASP* 1.3 61.4 + - - +
60B PRO* 3.5 8.5 - - + -
68B ALA* 3.4 1.2 - - - -
69B ILE* 2.8 43.9 + - + +
71B VAL* 3.8 41.1 - - + -
73B CYS* 4.6 4.0 - - - -
80B THR* 4.1 10.1 - - + -
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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