Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 4WJN
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 GLU 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 2.8 51.5 + - + +
26A VAL 3.3 6.1 - - - +
27A ILE* 4.5 8.8 - - + +
31A SER 3.9 9.2 - - - +
32A SER* 1.3 80.6 - - - +
34A ILE* 1.3 64.5 + - - +
35A HIS* 3.8 16.0 + - + -
51A TYR* 5.9 0.2 - - - -
8B GLU 5.5 0.9 - - - +
10B ARG* 3.1 24.0 + - - +
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.8 0.2 - - - -
26A VAL* 2.8 34.8 + - - +
32A SER* 5.9 0.2 - - - +
33A GLU* 1.3 78.6 - - - +
35A HIS* 1.3 72.3 + - - +
36A PHE* 3.7 24.4 - - + -
51A TYR* 4.1 17.0 - - + -
54A ARG* 4.2 22.9 - - + -
55A GLN* 3.6 25.4 - - - +
10B ARG* 3.5 39.5 - - + +
12B VAL* 3.9 14.6 - - + -
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.9 30.3 - - + -
24A LEU 3.1 6.7 - - - +
25A LYS* 3.7 38.0 - - + -
33A GLU* 3.8 24.8 - - + +
34A ILE* 1.3 78.6 - - - +
36A PHE* 1.3 63.3 + - - +
85A GLU* 6.5 1.8 - - + -
9B GLU* 4.1 24.7 + - + +
10B ARG 2.9 21.1 + - - +
11B VAL* 3.4 9.8 - - + -
12B VAL 2.9 24.4 + - - -
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Residues in contact with PHE 36 (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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22A ILE 3.5 1.7 - - - +
23A LYS* 3.4 3.0 - - - -
24A LEU* 2.8 35.3 + - + +
26A VAL* 3.5 31.0 - - + -
34A ILE* 3.7 28.9 - - + -
35A HIS* 1.3 74.1 - - - +
37A LYS* 1.3 62.8 + - - +
38A VAL* 3.9 5.5 + - + +
47A LEU* 3.6 28.0 - - + -
50A SER* 3.5 28.0 - - - -
51A TYR* 3.9 30.7 - + + -
54A ARG* 4.8 2.0 - - - -
12B VAL* 3.2 24.0 - - + +
14B ILE* 3.8 17.5 - - + -
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Residues in contact with LYS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.7 32.3 - - + -
22A ILE 3.3 8.7 - - - +
23A LYS* 4.1 30.8 - - + +
36A PHE* 1.3 74.5 - - - +
38A VAL* 1.3 63.0 + - - +
11B VAL* 4.1 18.4 - - + +
12B VAL 2.8 13.3 + - - +
13B VAL* 4.3 16.8 - - + -
14B ILE* 2.9 29.3 + - - +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.3 8.7 - - - -
22A ILE* 2.8 36.5 + - + +
24A LEU* 3.7 26.5 - - + -
36A PHE* 4.4 2.9 - - + +
37A LYS* 1.3 80.8 - - - +
39A LYS* 1.3 61.0 + - - +
42A THR* 3.8 18.4 - - + +
44A LEU* 4.6 3.6 - - + -
47A LEU* 4.2 19.5 - - + -
77A PRO* 3.8 18.8 - - + -
14B ILE* 3.8 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