Contacts of the strand formed by residues 28 - 31 (chain B) in PDB entry 3NER
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 ARG 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP 3.0 28.9 + - - -
61A VAL* 3.1 26.8 + - - +
62A GLY* 4.0 4.2 - - - +
4B VAL* 5.7 3.6 - - - +
24B VAL* 3.2 6.5 - - - +
25B ILE 2.9 32.9 + - - +
26B HIS* 3.8 9.2 - - - +
27B GLY* 1.3 84.1 - - - +
29B VAL* 1.3 63.0 + - - +
30B TYR* 3.6 25.1 + - + +
75B TYR* 3.5 16.8 + - + -
77B GLY 3.6 7.0 - - - +
78B ASP* 3.2 29.6 + - - +
302B SO4 3.4 23.8 + - - -
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Residues in contact with VAL 29 (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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7B TYR* 4.2 8.5 - - + -
12B VAL* 4.0 13.9 - - + -
22B TRP* 3.8 33.9 - - + -
23B LEU 3.4 8.1 - - - +
24B VAL* 4.6 2.0 - - + -
28B ARG* 1.3 76.6 - - - +
30B TYR* 1.3 64.4 + - - +
75B TYR* 3.7 4.3 - - - -
76B ILE* 2.8 39.9 + - + +
77B GLY 2.8 16.7 + - - +
78B ASP 4.0 4.9 - - - +
79B ILE* 3.9 38.6 - - + +
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Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 3.1 7.2 - - - +
23B LEU* 2.9 39.6 + - + +
25B ILE* 3.6 29.5 + - + +
26B HIS* 5.9 0.5 - - - +
28B ARG* 3.6 46.3 + - + +
29B VAL* 1.3 74.4 - - - +
31B ASP* 1.3 61.4 + - - +
32B VAL* 3.6 18.8 + - + +
71B LEU* 3.3 58.5 - - + +
72B LYS* 4.6 1.3 - - - +
74B TYR* 3.2 6.7 - - + +
75B TYR* 3.4 27.1 - + + -
76B ILE* 4.6 1.1 - - - -
201B HEM 4.9 0.4 - - + -
302B SO4 4.8 2.6 + - - -
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 5.0 3.6 - - - +
21B LEU 3.5 1.7 - - - +
22B TRP* 3.5 28.2 + - - +
30B TYR* 1.3 69.1 - - - +
32B VAL* 1.3 57.9 + - - +
33B THR* 2.7 32.3 + - - -
34B ARG* 3.7 14.9 + - - +
74B TYR* 2.9 28.9 + - - +
76B ILE* 3.9 24.2 - - + +
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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