Contacts of the strand formed by residues 41 - 50 (chain B) in PDB entry 1KR2
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 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LYS* 3.9 10.1 + - - +
7B THR* 3.3 24.7 - - + +
9B VAL* 3.7 21.5 - - + -
35B MET* 3.6 46.4 - - + +
36B ASN* 3.5 20.6 - - - +
38B THR* 3.3 22.9 + - + -
39B GLY 3.6 0.8 - - - -
40B ARG* 1.3 114.9 + - + +
42B THR* 1.3 67.4 + - - +
152B LYS* 4.4 14.7 - - - -
208B SER 4.9 2.9 + - - -
209B ASN* 5.5 2.4 + - - -
211B HIS* 3.5 21.7 + + - -
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Residues in contact with THR 42 (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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6B LYS* 3.3 27.0 + - - +
7B THR 3.1 7.4 + - - -
8B GLU* 3.3 14.4 - - + +
9B VAL* 2.8 26.7 + - - -
36B ASN* 3.4 6.5 - - - +
41B TYR* 1.3 77.3 + - - +
43B VAL* 1.3 65.7 + - - +
44B VAL* 3.3 16.0 + - + +
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Residues in contact with VAL 43 (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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9B VAL* 3.4 16.8 - - + +
11B LEU* 4.0 17.0 - - + -
32B LYS* 3.9 35.1 + - + +
35B MET* 3.7 32.3 - - + -
36B ASN* 3.0 16.7 + - - +
42B THR* 1.3 72.7 - - - +
44B VAL* 1.3 62.6 + - - +
45B LYS 4.0 4.5 - - - +
79B TRP* 3.4 34.2 - - + +
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Residues in contact with VAL 44 (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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8B GLU* 3.7 29.8 - - + +
9B VAL 2.9 17.7 + - - +
10B VAL* 3.9 17.3 - - + -
42B THR* 3.3 21.1 + - + +
43B VAL* 1.3 74.6 - - - +
45B LYS* 1.3 70.2 + - + +
79B TRP* 4.9 8.9 - - - +
149B PRO* 4.5 14.1 - - + -
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Residues in contact with LYS 45 (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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9B VAL 3.8 0.9 + - - +
10B VAL* 3.3 12.8 - - + +
11B LEU* 2.9 25.3 + - - +
43B VAL* 3.5 4.5 - - - +
44B VAL* 1.3 93.5 - - + +
46B GLY* 1.3 71.9 + - - +
47B ILE* 4.0 20.1 - - + +
79B TRP* 3.6 20.4 - - - +
81B GLU* 3.7 31.8 + - - +
106B LEU* 5.0 14.1 - - + +
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Residues in contact with GLY 46 (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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11B LEU* 3.3 6.7 - - - -
28B PHE* 3.7 17.3 - - - -
45B LYS* 1.3 77.0 - - - +
47B ILE* 1.3 66.8 + - - +
79B TRP* 2.9 24.2 + - - +
80B VAL* 3.4 2.8 - - - -
81B GLU* 2.8 26.9 + - - +
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Residues in contact with ILE 47 (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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10B VAL* 3.4 25.8 - - + -
11B LEU 2.7 10.5 + - - +
12B LEU* 3.6 22.5 - - + +
13B ALA 2.9 27.0 + - - -
28B PHE* 3.6 4.1 - - - -
45B LYS* 4.0 18.8 - - + +
46B GLY* 1.3 79.1 - - - +
48B ILE* 1.3 67.3 + - - +
49B SER* 4.7 0.4 - - - -
81B GLU* 3.2 10.8 - - + +
82B VAL 4.9 0.2 - - - -
83B ASP* 3.7 28.9 - - + -
102B HIS* 4.0 23.6 - - + +
106B LEU* 6.0 4.3 - - + -
151B VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 48 (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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13B ALA 3.8 3.1 - - - -
17B PHE* 3.7 31.6 - - + -
20B ILE* 3.6 26.9 - - + -
24B HIS* 5.4 1.1 - - + -
25B LEU* 4.3 5.2 - - + -
28B PHE* 3.4 31.6 - - + -
47B ILE* 1.3 73.2 - - - +
49B SER* 1.3 60.1 + - - +
50B PRO* 3.4 15.2 - - + +
70B ALA* 4.3 10.3 - - + -
74B THR* 4.0 21.1 - - + -
80B VAL* 4.0 6.5 - - + -
81B GLU 2.8 10.5 + - - +
82B VAL* 3.2 8.3 - - + -
83B ASP 3.0 22.5 + - - -
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Residues in contact with SER 49 (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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12B LEU* 4.1 18.8 - - - -
13B ALA 3.0 14.1 + - - -
14B CYS* 3.6 15.6 - - - -
15B GLY 3.7 1.4 + - - -
17B PHE* 4.2 2.2 - - - -
47B ILE* 3.8 3.8 + - - -
48B ILE* 1.3 72.8 - - - +
50B PRO* 1.3 65.0 - - - +
51B VAL 3.6 1.0 + - - -
83B ASP* 3.6 11.9 + - - -
86B GLU* 2.7 43.7 + - - +
98B VAL* 4.1 5.9 - - - +
102B HIS* 4.9 4.7 + - - -
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Residues in contact with PRO 50 (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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15B GLY 3.5 7.6 - - - +
16B SER 4.7 0.9 - - - +
17B PHE* 3.8 9.6 - - + -
48B ILE* 3.4 22.7 - - + +
49B SER* 1.3 87.8 + - - +
51B VAL* 1.3 65.9 + - - +
66B ARG* 4.1 20.2 - - + +
67B VAL* 4.2 26.7 - - + -
70B ALA* 4.3 14.8 - - + -
82B VAL* 4.0 7.6 - - + -
83B ASP 3.9 8.7 - - - +
86B GLU* 4.0 3.5 - - - +
87B SER* 3.6 21.9 + - - -
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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