Contacts of the strand formed by residues 30 - 34 (chain B) in PDB entry 2CGA
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 GLN 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TRP* 2.9 27.4 + - + +
28B PRO 4.6 3.3 - - - +
29B TRP* 1.3 84.7 - - + +
31B VAL* 1.4 85.9 + - - +
43B GLY* 4.2 4.9 - - - -
44B GLY 3.6 13.8 + - - +
67B VAL 4.5 2.1 - - - +
68B ALA* 5.2 0.2 - - - +
69B GLY 4.6 10.7 + - - -
70B GLU 5.4 2.3 + - - +
139B THR* 2.8 39.6 + - - +
140B GLY* 3.9 1.7 - - - -
141B TRP* 3.6 34.3 - - + -
155B LEU* 4.0 13.4 - - + +
194B ASP* 4.5 4.0 + - - -
197B GLY* 4.9 0.2 - - - -
198B PRO* 3.6 14.4 - - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP 3.6 9.9 - - - +
30B GLN* 1.4 96.0 + - - +
32B SER* 1.3 60.9 + - - +
33B LEU* 4.4 5.6 - - + -
43B GLY* 3.4 3.6 - - - -
44B GLY* 2.9 41.7 + - - +
46B LEU* 3.7 28.5 - - + +
52B VAL* 3.9 14.1 - - + -
66B VAL* 3.7 26.2 - - + -
67B VAL 3.3 13.2 - - - +
68B ALA* 4.1 6.7 - - + -
141B TRP* 3.9 5.8 - - - -
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Residues in contact with SER 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 1.3 74.2 - - - +
33B LEU* 1.3 61.7 + - - +
34B GLN* 3.1 21.2 + - - +
40B HIS* 2.8 27.5 + - - +
42B CYS 3.9 3.6 - - - -
66B VAL* 3.5 2.8 - - - -
67B VAL* 2.6 40.5 + - - +
70B GLU* 3.1 23.7 + - - -
73B GLN* 4.9 1.6 + - - -
141B TRP* 4.3 8.9 - - - -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B VAL* 4.4 9.9 - - + -
32B SER* 1.3 75.5 - - - +
34B GLN* 1.3 62.8 + - - +
40B HIS* 3.4 3.3 - - - -
41B PHE* 2.9 42.6 + - + -
42B CYS* 2.9 28.6 + - + +
43B GLY 3.7 19.7 - - - +
52B VAL* 5.0 2.2 - - + -
54B THR* 3.8 13.2 - - + +
60B VAL* 3.7 30.5 - - + -
64B ASP* 5.5 2.0 - - + -
65B VAL 3.4 4.7 - - - +
66B VAL* 3.5 32.3 - - + -
85B ILE* 5.5 0.4 - - + -
106B LEU* 4.2 8.1 - - + -
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B SER* 3.1 19.7 + - - +
33B LEU* 1.3 78.0 - - - +
35B ASP* 1.3 68.1 + - - +
38B GLY* 3.9 16.5 - - - +
39B PHE 3.2 3.8 - - - +
40B HIS* 3.7 19.3 - - - +
41B PHE* 3.9 3.8 - - - -
64B ASP* 3.6 5.9 - - - +
65B VAL* 3.0 42.1 + - + +
67B VAL* 3.3 19.2 - - + +
70B GLU* 3.2 22.0 + - - -
73B GLN* 5.0 5.5 - - - +
82B LYS* 3.6 16.5 + - - -
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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