Contacts of the strand formed by residues 26 - 30 (chain G) in PDB entry 3S4S
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 PHE 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24G ILE 3.1 5.1 + - - +
25G GLN* 1.3 77.0 - - - +
27G HIS* 1.3 74.7 + - - +
28G TRP* 3.9 15.3 - + - -
37G LEU* 3.8 24.5 - - + -
38G GLY* 3.2 26.2 - - - -
39G ASN* 3.2 41.3 + - - +
45G TRP* 4.5 0.7 - - - -
57G SER* 4.0 5.4 - - - -
62G TRP* 3.5 27.1 - + - -
67G PHE* 3.1 52.5 - + + -
84G CYS* 4.6 3.4 - - - -
85G GLU 3.5 11.4 - - - +
86G VAL* 4.2 11.2 - - + -
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Residues in contact with HIS 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G GLN* 6.1 2.2 - - - +
26G PHE* 1.3 84.7 + - - +
28G TRP* 1.3 66.7 + - - +
29G LYS* 3.4 22.6 - - + -
35G LYS* 3.5 28.9 + - + +
37G LEU 3.1 13.9 - - - +
45G TRP* 3.6 21.5 - + + -
84G CYS* 3.3 2.8 - - - -
85G GLU* 2.9 68.1 + - + +
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Residues in contact with TRP 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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14G LEU* 3.3 35.7 - - + -
15G THR 3.5 15.7 - - - -
16G CYS* 3.4 18.2 - - + -
26G PHE* 3.9 16.0 - + - -
27G HIS* 1.3 78.2 - - - +
29G LYS* 1.3 65.6 + - - +
35G LYS* 3.7 2.4 - - - +
36G ILE* 2.8 32.7 + - + +
37G LEU* 2.8 21.6 + - + +
67G PHE 2.9 19.3 + - - -
68G PRO 3.8 2.2 + - - -
69G LEU* 3.4 40.1 - - + +
82G TYR* 3.9 11.2 - - + -
83G ILE 3.4 3.1 - - - -
84G CYS* 3.6 32.0 - - + -
91G GLU* 5.2 0.9 - - + -
93G VAL* 3.5 26.5 - - + -
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Residues in contact with LYS 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 HIS* 3.4 26.3 + - + -
28G TRP* 1.3 79.4 - - - +
30G ASN* 1.3 67.6 + - - +
33G GLN* 3.5 40.0 + - - +
34G ILE 3.4 8.3 - - - +
35G LYS* 3.5 33.2 - - + +
36G ILE* 3.8 5.4 - - - -
82G TYR* 3.3 7.8 - - - +
83G ILE* 2.8 40.9 + - + +
85G GLU* 3.4 21.8 + - - +
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Residues in contact with ASN 30 (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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29G LYS* 1.3 77.7 - - - +
31G SER* 1.3 56.1 + - - +
32G ASN* 3.1 12.5 + - - +
33G GLN* 2.7 26.0 + - - +
34G ILE* 2.8 41.0 + - - +
36G ILE* 3.9 12.4 - - + +
49G SER* 4.7 4.4 + - - -
50G LYS* 3.2 43.4 - - + +
80G ASP* 3.3 13.2 - - - +
81G THR 3.6 5.4 - - - -
82G TYR* 4.4 7.9 - - + -
83G ILE* 3.8 6.8 - - - +
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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