Contacts of the strand formed by residues 32 - 37 (chain D) in PDB entry 1KGC
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 ILE 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24D HIS* 3.8 26.7 - - + +
27D ILE* 3.9 16.4 - - + -
31D TYR* 1.3 73.4 - - - +
33D HIS* 1.3 65.9 + - - +
34D TRP* 3.6 28.2 - - + +
48D HIS* 3.1 4.7 - - - +
49D GLY 2.9 34.3 + - - +
64D LEU* 4.0 14.3 - - + +
66D ILE* 4.5 4.7 - - + -
73D SER* 3.4 20.4 - - - +
90D CYS* 4.3 10.3 - - - -
91D ILE 3.7 6.1 - - - +
92D LEU* 3.8 26.0 - - + -
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Residues in contact with HIS 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 TYR* 3.6 22.4 - + + -
32D ILE* 1.3 77.4 - - - +
34D TRP* 1.3 64.8 - - - +
35D TYR* 4.3 21.5 - + + -
45D TYR* 5.0 3.4 - + - -
47D ILE 3.6 3.6 - - - -
48D HIS* 3.4 30.7 - + + -
89D TYR 3.6 0.7 - - - +
90D CYS* 3.6 2.8 - - - -
91D ILE* 2.8 50.9 + - + +
93D PRO* 3.5 32.0 - - + +
104D LEU* 4.5 14.1 - - + +
98E GLN 5.8 1.6 + - - -
105E GLU* 6.4 1.3 - - - -
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Residues in contact with TRP 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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5D GLN* 3.5 25.4 - - - -
20D LEU* 3.3 35.7 - - + -
21D PRO 4.2 0.4 - - - -
22D CYS* 3.9 14.6 - - + -
32D ILE* 3.6 10.8 - - + +
33D HIS* 1.3 79.1 - - - +
35D TYR* 1.3 66.4 + - - +
45D TYR* 4.2 0.2 - - - -
46D VAL* 2.9 26.0 + - + +
47D ILE* 2.8 28.7 + - + +
64D LEU* 3.5 31.9 - - + +
73D SER* 4.7 1.0 - - - -
74D THR* 4.2 3.3 - - - -
75D LEU* 3.5 44.8 - - + +
88D TYR* 4.1 16.2 - + + -
89D TYR 3.2 17.5 - - - -
90D CYS* 3.8 21.3 - - + -
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Residues in contact with TYR 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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33D HIS* 4.3 16.2 - + + -
34D TRP* 1.3 81.5 - - - +
36D ARG* 1.3 61.6 + - - +
43D PRO* 4.9 0.2 - - + -
44D GLU 3.3 12.3 - - - +
45D TYR* 3.4 44.4 - + + -
46D VAL* 4.0 3.1 - - - -
88D TYR* 3.5 4.5 - - - +
89D TYR* 2.8 33.4 + - + +
91D ILE* 4.1 14.4 - - + -
104D LEU* 3.7 25.2 - - + +
106D PHE* 3.8 28.7 - + + -
105E GLU* 3.6 11.3 - - - +
106E GLN* 3.0 35.1 + - + -
108E PHE* 4.2 13.2 - + - -
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Residues in contact with ARG 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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35D TYR* 1.3 75.3 - - - +
37D GLN* 1.3 61.3 + - - +
38D LEU* 3.7 19.2 - - + +
43D PRO* 3.2 3.0 - - - +
44D GLU* 2.6 68.6 + - + +
46D VAL* 3.7 12.4 - - + +
61D MET* 3.1 35.2 - - - +
83D ARG* 4.7 16.2 + - - +
84D ASP* 3.0 28.9 + - - +
86D ALA* 4.6 1.1 - - + -
87D VAL 3.1 11.4 - - - +
88D TYR* 3.1 43.0 + - + -
89D TYR* 4.4 2.9 - - - -
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Residues in contact with GLN 37 (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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36D ARG* 1.3 78.2 - - - +
38D LEU* 1.3 65.1 + - - +
39D PRO* 4.0 0.3 - - - +
41D GLN 3.0 28.5 + - - +
42D GLY* 4.2 1.5 - - - -
43D PRO* 3.7 27.5 - - + +
86D ALA* 3.2 3.7 - - - +
87D VAL* 2.8 35.2 + - + +
89D TYR* 2.7 41.3 + - + +
37E GLN* 2.9 33.5 + - - -
91E LEU* 4.4 2.4 - - - +
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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