Contacts of the strand formed by residues 5 - 10 (chain G) in PDB entry 1GUL
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 PRO 5 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ARG* 1.4 84.0 - - - +
6G LYS* 1.3 56.9 - - - +
7G LEU* 4.2 9.4 - - + -
23G LEU* 4.5 7.4 - - + -
28G VAL* 4.2 18.6 - - + -
29G GLU 3.5 18.8 - - - +
30G PHE* 3.2 10.8 - - + +
31G ASP 2.5 33.8 + - - -
58G VAL* 4.3 9.0 - - + -
59G GLU 3.2 13.9 - - - +
60G ILE* 4.0 25.8 - - + -
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Residues in contact with LYS 6 (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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4G ARG 3.5 4.9 + - - +
5G PRO* 1.3 74.9 - - - +
7G LEU* 1.3 66.3 + - - +
8G HIS* 3.7 12.1 - - - +
31G ASP* 3.4 26.0 - - + +
32G GLU 5.3 3.2 + - - -
33G GLU* 3.3 38.8 + - + +
58G VAL* 3.2 4.0 - - - -
59G GLU* 2.7 61.2 + - + +
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Residues in contact with LEU 7 (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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5G PRO 4.2 2.5 - - - -
6G LYS* 1.3 83.1 - - - +
8G HIS* 1.3 63.2 + - - +
9G TYR* 3.7 2.3 + - + +
16G MET* 3.7 36.8 - - + -
19G VAL* 4.4 9.0 - - + -
20G ARG* 4.0 11.4 - - + -
23G LEU* 4.1 14.6 - - + -
30G PHE* 3.9 28.0 - - + -
31G ASP 2.9 19.3 + - - +
32G GLU* 3.4 13.1 - - + +
33G GLU 2.7 30.3 + - - +
34G PHE* 5.4 0.5 - - - -
57G MET 3.9 1.6 - - - -
58G VAL* 3.9 18.4 - - + -
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Residues in contact with HIS 8 (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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6G LYS* 3.7 17.4 - - + +
7G LEU* 1.3 71.6 - - - +
9G TYR* 1.3 71.7 + - - +
16G MET* 3.3 10.4 - - - +
33G GLU* 3.6 47.1 + - + +
35G LEU* 4.9 0.6 - - + +
44G LEU* 4.0 34.3 - - + +
55G VAL* 3.6 17.5 - - + +
57G MET* 3.0 41.4 + - + +
59G GLU* 2.9 27.5 + - - +
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Residues in contact with TYR 9 (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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7G LEU* 3.7 3.0 + - + +
8G HIS* 1.3 80.5 - - - +
10G PRO* 1.3 100.4 - - + +
12G GLY 3.7 8.7 - - - -
13G ARG 3.6 17.0 - - - -
14G GLY* 3.7 9.3 - - - -
15G ARG* 2.9 29.5 + - - +
16G MET* 3.5 31.6 - - + -
20G ARG* 3.9 3.8 - - - +
33G GLU 3.5 4.9 + - - -
34G PHE* 3.1 13.5 - - + -
35G LEU* 2.9 24.9 + - - +
55G VAL* 3.9 17.0 - - + -
56G PRO* 3.5 24.5 - - + +
212G TYR* 4.2 8.3 - - - -
220G PHE* 5.6 1.8 - + - -
301G IBG 3.7 18.2 - - + +
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Residues in contact with PRO 10 (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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9G TYR* 1.3 128.0 - - + +
11G ASN* 1.3 61.5 + - - +
12G GLY 3.0 7.3 + - - -
20G ARG* 3.7 2.4 + - - -
34G PHE* 3.6 2.9 - - - -
35G LEU* 3.3 29.8 - - + +
55G VAL* 4.6 0.2 - - + -
212G TYR* 4.2 18.2 - - + +
215G THR* 5.2 2.7 - - + -
216G VAL* 4.5 11.4 - - + -
219G ILE* 4.6 11.2 - - + -
220G PHE* 4.1 26.9 - - + -
301G IBG 6.6 0.4 - - + -
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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