Contacts of the strand formed by residues 29 - 32 (chain A) in PDB entry 1CG4
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 TYR 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.7 9.5 - - - +
28A LYS* 1.3 94.4 - - + +
30A VAL* 1.3 61.8 + - - +
31A VAL* 4.6 6.5 - - + -
64A VAL* 3.6 3.4 - - - -
65A THR* 3.3 35.2 - - + +
67A ILE* 3.9 7.9 - - + -
98A LEU* 5.8 0.2 - - + -
207A LEU* 3.5 38.4 - - + +
208A LEU* 5.3 0.9 - - + -
211A ALA* 3.5 27.8 - - + -
214A ARG* 2.9 25.1 + - - -
216A ASP* 4.1 2.9 - - + -
217A PHE 3.2 2.4 + - - -
218A VAL* 3.5 22.5 - - + -
219A MET 3.0 22.1 + - - -
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Residues in contact with VAL 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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20A VAL* 3.6 30.5 - - + -
24A THR* 4.0 15.7 - - + -
29A TYR* 1.3 75.7 - - - +
31A VAL* 1.3 65.1 + - - +
32A ARG 4.4 0.2 - - - -
56A PRO* 3.7 9.3 - - + +
58A GLY* 3.7 13.2 - - - +
64A VAL* 3.8 3.6 - - + +
65A THR 3.1 6.2 + - - +
66A SER* 3.0 32.1 - - - +
67A ILE 2.7 27.4 + - - +
219A MET* 3.1 11.0 - - + +
221A GLU* 4.3 13.2 - - + +
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Residues in contact with VAL 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 TYR* 4.6 0.7 - - + -
30A VAL* 1.3 83.2 - - - +
32A ARG* 1.3 73.1 + - - +
33A TYR* 3.7 2.1 - - - -
56A PRO* 5.1 0.2 - - - -
67A ILE* 3.4 28.9 - - + +
69A GLY* 4.3 3.4 - - - +
204A VAL* 5.0 2.9 - - + -
208A LEU* 4.1 11.9 - - + -
218A VAL* 4.0 20.2 - - + -
219A MET 2.7 14.8 + - - +
220A PHE* 3.3 24.9 - - + -
221A GLU* 2.6 34.2 + - - +
252A SER* 4.3 15.5 - - - -
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Residues in contact with ARG 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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30A VAL 4.4 0.2 - - - -
31A VAL* 1.3 75.3 - - - +
33A TYR* 1.3 58.3 + - - +
34A GLN 2.9 27.4 + - - -
35A GLY 3.7 1.4 - - - -
36A GLY* 3.0 28.5 + - - +
39A ALA* 3.9 5.6 - - - +
41A HIS* 4.0 5.6 + - - -
53A HIS 2.7 28.7 + - - -
54A LEU* 3.8 13.0 + - - +
55A ILE 4.9 1.6 + - - -
56A PRO* 3.8 23.0 - - + +
67A ILE 2.9 11.8 + - - +
68A ILE* 4.5 4.0 - - + -
69A GLY* 2.8 28.6 + - - -
72A VAL* 3.7 14.9 - - + +
221A GLU* 3.6 36.4 + - - +
223A ALA* 3.3 22.2 - - - +
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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