Contacts of the strand formed by residues 23 - 30 (chain A) in PDB entry 2JYA
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 TRP 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.5 28.5 - - + -
6A TYR 3.3 20.2 - - - -
7A ARG* 3.5 29.3 - - + +
21A ASN 4.8 1.3 - - - -
22A VAL* 1.3 70.3 - - - +
24A VAL* 1.3 61.8 + - - +
25A LEU 4.0 0.3 + - - -
53A LEU 4.0 0.2 - - - +
54A THR* 3.4 3.8 - - - -
55A PHE* 3.0 40.5 + - + +
56A GLU 3.4 25.2 + - - -
57A THR* 3.5 15.5 - - - +
58A GLN* 3.4 46.0 - - + +
61A ALA* 5.1 1.1 - - + -
74A VAL* 4.8 1.1 - - + -
75A ILE 4.0 18.6 - - - -
76A LEU* 5.0 0.4 - - + -
77A PRO* 3.6 27.8 - - + -
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Residues in contact with VAL 24 (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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4A LYS 3.4 0.2 - - - +
5A ILE* 3.6 1.7 - - - -
6A TYR* 2.8 65.0 + - + +
8A PRO* 4.1 15.7 - - + -
12A ALA* 3.8 33.9 - - + +
22A VAL* 4.0 10.5 - - + +
23A TRP* 1.3 74.8 - - - +
25A LEU* 1.3 61.8 + - - +
26A GLU 3.9 0.2 - - - -
52A LYS* 3.7 28.0 - - + -
53A LEU 3.5 10.3 - - - +
54A THR* 4.5 5.4 - - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 3.7 25.1 - - + -
4A LYS 3.3 5.8 - - - +
5A ILE* 3.6 23.8 - - + +
23A TRP 4.0 0.4 + - - -
24A VAL* 1.3 70.1 - - - +
26A GLU* 1.3 58.5 + - - +
27A PHE* 3.9 9.7 - - + -
51A VAL 3.9 0.5 - - - +
52A LYS* 3.1 4.6 - - - -
53A LEU* 2.9 42.4 + - + +
55A PHE* 3.7 20.0 - - + -
61A ALA* 3.3 38.1 - - + +
64A TYR* 3.5 28.9 - - + -
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Residues in contact with GLU 26 (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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2A SER 4.0 0.7 - - - +
3A ALA* 3.5 0.7 - - - -
4A LYS* 2.8 74.1 + - + +
6A TYR* 3.8 13.8 + - - +
24A VAL 3.9 1.2 - - - -
25A LEU* 1.3 73.1 - - - +
27A PHE* 1.3 64.2 + - - +
50A GLN* 4.0 33.2 - - + +
51A VAL 3.4 11.2 - - - +
52A LYS* 3.1 32.9 + - + -
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Residues in contact with PHE 27 (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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2A SER 3.4 6.1 - - - +
3A ALA* 3.7 21.5 - - + +
4A LYS* 6.0 0.4 - - - +
25A LEU* 3.9 11.9 - - + -
26A GLU* 1.3 78.9 - - - +
28A ASP* 1.3 56.8 + - - +
29A ALA* 2.9 39.2 + - + -
50A GLN* 3.3 22.1 - - - -
51A VAL* 3.1 34.5 + - + -
53A LEU* 4.0 22.9 - - + -
64A TYR* 3.4 37.0 - + - -
70A ILE* 3.8 24.7 - - + -
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.3 37.8 - - + +
2A SER* 3.2 29.5 + - - +
27A PHE* 1.3 74.0 - - - +
29A ALA* 1.3 59.9 + - - +
30A GLU 3.4 0.7 + - - -
48A LYS* 2.9 51.1 + - - +
49A GLN 3.9 4.7 - - - -
50A GLN* 4.9 2.4 - - - +
70A ILE* 5.3 0.9 - - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 2.9 17.8 + - + +
28A ASP* 1.3 68.9 - - - +
30A GLU* 1.3 64.9 + - - +
31A VAL 3.3 1.6 + - - -
48A LYS* 3.5 1.7 - - - +
49A GLN* 2.8 55.4 + - + +
51A VAL* 3.7 30.1 - - + -
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Residues in contact with GLU 30 (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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1A MET* 3.4 40.7 - - + +
28A ASP 3.4 4.2 + - - -
29A ALA* 1.3 69.6 - - - +
31A VAL* 1.3 61.2 + - - +
32A PRO* 3.4 20.1 - - + +
48A LYS* 3.9 13.5 - - + -
49A GLN* 5.5 1.0 + - - -
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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