Contacts of the strand formed by residues 21 - 29 (chain G) in PDB entry 3M4D
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 LYS 21 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LYS 5.8 1.1 - - - -
47F ASN* 3.6 27.4 - - - +
19G THR* 3.9 9.8 + - + +
20G VAL* 1.3 74.8 - - - +
22G THR* 1.3 60.9 + - - +
40G TYR* 4.8 0.9 - - - -
41G SER* 3.3 1.2 - - - -
42G PHE* 2.7 42.1 + - + +
288G LYS 3.5 13.1 + - - -
289G GLU* 3.3 53.6 + - + +
290G GLU* 4.8 4.9 + - - +
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Residues in contact with THR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F THR 3.9 15.0 - - - +
13F ASP 5.3 2.2 - - - +
14F ILE* 3.8 7.6 - - + +
45F ASP* 5.1 1.4 + - - -
47F ASN 2.9 7.5 + - - +
48F HIS* 2.6 37.0 + - - +
49F ASN* 3.0 21.1 + - - +
20G VAL* 3.9 17.5 - - + +
21G LYS* 1.3 79.0 - - - +
23G GLY* 1.3 59.3 + - - +
39G PHE* 4.1 5.2 - - + -
40G TYR* 3.2 17.0 + - - -
41G SER* 3.5 19.7 - - - +
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Residues in contact with GLY 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F HIS* 3.4 7.6 + - - -
49F ASN* 3.1 18.2 - - - -
22G THR* 1.3 79.4 - - - +
24G ASP* 1.3 60.8 + - - -
39G PHE* 3.3 7.4 - - - -
40G TYR* 2.9 47.4 + - - +
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Residues in contact with ASP 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F HIS* 3.9 14.8 + - - +
49F ASN* 2.8 13.8 + - - +
50F LYS* 2.9 22.0 + - + -
52F LEU* 6.4 0.4 - - - -
99F SER* 2.5 25.3 + - - -
233F THR* 3.8 15.8 + - + +
23G GLY* 1.3 73.5 - - - -
25G LEU* 1.3 67.7 + - - +
26G VAL* 3.4 20.8 - - - +
37G LYS* 2.6 31.4 + - - +
38G VAL 3.4 2.7 - - - -
39G PHE* 3.8 12.0 - - - -
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F ASN* 3.7 6.7 - - - +
50F LYS* 4.1 4.5 - - - +
24G ASP* 1.3 85.2 + - - +
26G VAL* 1.3 62.8 + - - +
27G THR* 5.2 0.9 - - - -
36G LYS 3.7 1.0 - - - +
37G LYS* 3.3 2.8 - - - -
38G VAL* 2.9 41.3 + - + +
40G TYR* 3.2 33.4 - - + -
282G TYR* 3.5 41.2 + - + -
291G MET* 3.6 29.2 - - + +
292G THR* 4.0 7.6 - - - -
293G ASN* 4.3 13.0 - - - +
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Residues in contact with VAL 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LYS* 4.4 5.6 - - - +
97F GLN* 3.3 28.9 + - + +
98F ILE 3.7 6.5 - - - +
99F SER* 3.8 16.6 - - - -
162F ASP* 3.8 17.9 - - + -
233F THR* 4.7 4.3 - - - +
24G ASP* 3.4 23.3 - - - +
25G LEU* 1.3 72.3 - - - +
27G THR* 1.3 69.6 + - - +
35G HIS* 3.5 28.0 - - + +
36G LYS 3.4 4.0 - - - +
37G LYS* 3.6 16.4 - - + -
293G ASN* 4.9 3.3 + - - +
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Residues in contact with THR 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F GLN* 5.1 1.1 - - - +
25G LEU 5.2 0.2 - - - -
26G VAL* 1.3 79.9 + - - +
28G TYR* 1.3 68.8 + - - +
29G ASP* 5.5 1.6 - - + -
34G MET 3.7 0.5 - - - +
35G HIS* 4.1 0.2 - - - -
36G LYS* 2.8 50.1 + - - +
280G GLU* 2.9 41.9 + - - +
282G TYR* 4.3 3.3 + - - -
293G ASN* 3.3 9.7 + - - -
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Residues in contact with TYR 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PRO 3.7 7.7 + - - -
161F THR* 3.4 47.9 - - + +
162F ASP* 3.4 34.9 + - + +
27G THR* 1.3 80.5 - - - +
29G ASP* 1.3 59.1 + - - +
30G LYS* 3.4 40.4 + - + +
33G GLY* 3.8 15.3 - - - -
34G MET 3.2 28.7 - - - -
35G HIS* 3.8 4.7 - - + -
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Residues in contact with ASP 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G THR* 4.0 2.8 + - + -
28G TYR* 1.3 69.9 - - - +
30G LYS* 1.3 60.0 + - - +
31G GLU* 3.3 7.3 + - - +
32G ASN* 2.7 41.1 + - + -
33G GLY 2.9 23.0 + - - -
34G MET* 3.0 23.4 + - + +
36G LYS* 4.6 6.5 - - - -
278G SER* 2.5 29.7 + - - +
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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