Contacts of the strand formed by residues 31 - 36 (chain D) in PDB entry 2Q9Q
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 31 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C GLU* 5.6 2.9 - - - -
29D HIS* 3.9 17.7 - - - +
30D GLU* 1.3 75.9 - - - +
32D LEU* 1.3 63.5 + - - +
33D PRO* 4.8 0.2 - - - +
67D GLU* 3.9 37.6 + - + +
68D LEU 3.0 11.0 - - - +
69D PRO* 3.3 38.4 - - + -
89D PRO* 4.9 3.5 - - - +
119D PHE* 4.0 8.3 - - - -
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS* 1.3 75.0 - - - +
33D PRO* 1.3 80.8 - - + +
34D VAL* 3.5 5.5 + - + +
66D LEU 3.6 0.2 - - - +
67D GLU* 4.0 4.7 - - - -
68D LEU 2.9 37.1 + - - +
70D LEU* 4.0 18.8 - - + -
73D ALA* 3.6 23.6 - - + -
86D VAL* 4.2 11.7 - - + -
87D GLU 4.6 2.0 - - - +
89D PRO* 4.3 6.1 - - + -
119D PHE* 3.8 12.1 - - + -
123D LEU* 4.1 14.1 - - + -
126D PHE* 3.5 33.0 - - + -
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Residues in contact with PRO 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS 4.8 0.2 - - - +
32D LEU* 1.3 86.5 - - + +
34D VAL* 1.3 62.3 + - - +
66D LEU 3.7 1.6 - - - +
67D GLU* 3.5 21.3 - - - +
86D VAL* 3.4 2.4 - - - +
87D GLU* 2.7 68.4 + - + +
88D LEU 4.9 1.1 - - - +
89D PRO* 4.0 20.6 - - + -
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.5 18.6 - - + +
33D PRO* 1.3 80.4 - - - +
35D ARG* 1.3 61.2 + - - +
36D THR 5.5 0.4 - - - +
65D LYS* 3.2 7.4 - - - +
66D LEU* 2.7 59.2 + - + +
68D LEU* 3.5 28.7 - - + -
73D ALA* 4.3 3.8 - - + -
84D LEU* 4.0 16.6 - - + -
85D SER 3.1 9.4 - - - +
86D VAL* 3.5 22.4 - - + +
87D GLU* 4.4 5.1 + - - +
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 1.3 75.4 - - - +
36D THR* 1.3 70.0 + - - +
37D GLU* 2.7 32.7 + - - +
63D GLY* 4.2 26.7 + - - +
64D SER 3.2 3.8 - - - +
65D LYS* 4.2 19.9 - - + +
81D ARG* 6.2 0.4 - - - -
84D LEU* 3.4 3.3 - - - -
85D SER* 2.7 47.9 + - - +
87D GLU* 4.4 12.8 - - + +
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Residues in contact with THR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D VAL* 5.5 1.0 - - - +
35D ARG* 1.3 70.0 - - - +
37D GLU* 1.3 68.2 + - - +
38D THR* 2.7 33.4 - - + +
40D MET* 3.5 32.2 - - + +
60D VAL* 4.0 4.4 - - + +
61D PRO 3.7 7.0 - - - +
62D GLN* 4.4 0.2 - - - +
63D GLY* 2.7 26.1 + - - -
64D SER* 2.6 41.2 + - - +
66D LEU* 4.0 5.7 - - - +
83D ILE 4.0 5.2 - - - +
84D LEU* 4.4 4.0 - - - -
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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