Contacts of the strand formed by residues 24 - 33 (chain A) in PDB entry 5N8A
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 ILE 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLN 3.3 25.6 - - - +
5A LEU* 3.6 4.5 - - + +
6A SER* 2.8 42.3 + - - +
22A LYS 4.4 0.7 - - - +
23A PRO* 1.3 74.3 - - - +
25A LEU* 1.3 63.6 + - - +
76A VAL* 3.5 28.0 - - + -
77A CYS 3.4 5.6 - - - +
78A GLN* 4.0 22.7 - - + +
102A LEU* 3.7 26.0 - - + -
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Residues in contact with LEU 25 (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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5A LEU* 4.0 5.8 - - - -
9A ALA* 4.5 4.9 - - + -
10A ILE* 4.6 6.1 - - + -
13A ILE* 5.5 3.8 - - + -
23A PRO* 4.3 23.1 - - + +
24A ILE* 1.3 84.8 - - - +
26A GLN* 1.3 60.6 + - - +
46A MET* 4.0 22.0 - - + -
47A SER 3.3 10.1 - - - +
48A ASP* 3.6 27.4 - - + -
56A PHE* 4.1 28.5 - - + -
76A VAL* 3.5 2.8 - - - +
77A CYS* 2.9 36.1 + - - +
79A ILE* 3.9 21.1 - - + -
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Residues in contact with GLN 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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5A LEU* 4.0 19.0 - - + +
25A LEU* 1.3 73.7 - - - +
27A VAL* 1.3 73.4 + - - +
28A ILE* 3.5 13.4 + - + +
46A MET* 3.3 5.3 - - - -
47A SER* 2.8 38.1 + - - +
74A ASN* 3.0 23.5 + - - +
75A CYS 3.4 13.0 - - - +
76A VAL* 4.3 2.9 - - + +
108A VAL* 3.5 9.5 - - - +
110A VAL 2.8 26.1 + - - -
111A LYS* 3.6 3.9 - - - +
112A ILE* 2.8 34.6 + - - +
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Residues in contact with VAL 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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25A LEU 4.2 0.4 + - - -
26A GLN* 1.3 72.6 - - - +
28A ILE* 1.3 60.5 + - - +
29A ASN 3.8 11.0 - - - +
30A ILE* 3.5 32.5 - - + -
44A LEU* 4.2 6.7 - - + -
45A LEU 4.0 3.1 - - - +
46A MET* 3.9 23.6 - - + -
71A LEU* 3.9 15.0 - - + -
72A SER 3.7 16.4 - - - +
73A SER* 4.0 3.1 - - - -
74A ASN* 2.7 32.2 + - - -
75A CYS* 2.9 29.7 + - - +
77A CYS* 4.3 2.9 - - - -
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Residues in contact with ILE 28 (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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26A GLN* 3.7 24.7 - - - +
27A VAL* 1.3 77.5 - - - +
29A ASN* 1.3 60.1 + - + +
45A LEU* 2.7 39.5 + - + +
46A MET 4.3 2.0 - - - -
47A SER* 3.8 29.4 - - - +
52A THR* 4.4 10.3 - - + -
73A SER* 3.4 17.0 + - - -
74A ASN* 4.6 4.5 + - - +
111A LYS* 3.8 34.5 - - + +
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Residues in contact with ASN 29 (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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27A VAL* 3.7 2.0 - - - +
28A ILE* 1.3 80.6 - - + +
30A ILE* 1.3 88.3 + - - +
31A ARG* 4.3 14.5 - - - +
43A ARG 5.6 0.4 + - - -
44A LEU* 3.3 4.2 - - - -
45A LEU* 2.9 44.2 + - + +
73A SER* 3.5 10.0 + - - -
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Residues in contact with ILE 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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27A VAL* 3.5 17.0 - - + -
29A ASN* 1.3 90.8 + - - +
31A ARG* 1.3 67.4 + - - +
42A TYR* 4.1 22.0 - - + -
43A ARG 3.4 11.2 - - - +
44A LEU* 4.0 11.7 - - + -
66A VAL* 4.2 22.0 - - + -
71A LEU* 3.4 38.4 - - + +
72A SER* 3.8 13.0 - - - -
73A SER* 4.0 7.2 + - - +
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Residues in contact with ARG 31 (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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29A ASN* 4.3 12.6 - - - +
30A ILE* 1.3 77.4 - - - +
32A PRO* 1.3 93.6 + - + +
34A THR* 5.3 0.2 + - - -
42A TYR* 3.5 7.1 - - - -
43A ARG* 2.9 61.8 + - + +
2X PRO* 5.9 0.4 - - - +
3X ASP* 2.9 38.7 + - - +
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Residues in contact with PRO 32 (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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31A ARG* 1.3 112.4 + - + +
33A ILE* 1.3 65.4 + - - +
40A PRO* 5.8 3.8 - - + -
41A ARG 3.3 11.0 - - - +
42A TYR* 3.8 19.9 - - + -
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Residues in contact with ILE 33 (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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32A PRO* 1.3 78.9 - - - +
34A THR* 1.3 77.1 + - - +
35A THR* 3.1 14.4 + - + +
40A PRO* 5.7 0.2 - - - +
41A ARG* 2.8 25.4 + - + +
42A TYR 3.8 11.9 - - - -
43A ARG* 3.7 26.5 - - + +
57A MET* 3.1 44.6 - - + -
3X ASP* 3.6 28.5 - - + +
6X ILE* 4.1 2.9 - - + -
7X ILE* 3.9 18.2 - - + -
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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