Contacts of the helix formed by residues 21 - 32 (chain B) in PDB entry 6K71
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 ALA 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B MET* 1.3 81.4 - - - +
22B SER* 1.3 65.1 + - - +
23B ALA* 3.2 11.2 - - + +
24B VAL* 3.3 18.6 - - + +
25B ALA* 3.5 8.0 + - - +
132B ARG* 4.1 24.9 - - + +
133B VAL* 6.0 2.5 - - + -
231B GLU* 5.7 4.5 - - + -
234B LYS* 4.4 19.3 - - - +
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Residues in contact with SER 22 (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 PHE* 3.5 20.0 - - - -
14B MET* 5.9 6.5 - - - -
21B ALA* 1.3 73.1 - - - +
23B ALA* 1.3 65.7 + - - +
25B ALA* 3.4 9.4 + - - +
26B ALA* 3.0 20.4 + - - +
60B ASP* 5.4 4.7 - - - -
62B SER* 4.9 7.3 + - - -
64B ALA* 4.1 14.1 - - - +
65B VAL* 5.2 3.4 - - - +
234B LYS* 5.4 0.7 + - - -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.2 5.7 - - + +
22B SER* 1.3 80.6 + - - +
24B VAL* 1.3 57.7 + - - +
26B ALA* 3.0 9.8 + - - +
27B ILE* 2.9 32.8 + - + +
64B ALA* 4.2 20.6 - - + +
67B SER* 5.0 2.5 - - - +
68B GLY* 5.6 1.2 - - - +
231B GLU* 5.8 5.4 - - + -
233B PHE 5.2 5.2 - - - +
234B LYS* 3.6 31.4 - - + +
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Residues in contact with VAL 24 (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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20B MET* 3.6 28.3 - - + -
21B ALA* 3.3 22.7 - - + +
23B ALA* 1.3 73.4 - - - +
25B ALA* 1.3 59.3 + - - +
27B ILE* 3.3 9.5 - - - +
28B ARG* 3.0 41.9 + - - +
101B LEU* 3.8 12.8 - - + -
104B ILE* 3.7 43.1 - - + +
105B SER* 4.7 1.6 - - - +
132B ARG* 6.1 0.4 - - - +
231B GLU* 6.4 1.1 - - + -
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Residues in contact with ALA 25 (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 PHE* 3.6 15.0 - - + -
13B GLN* 3.9 27.0 - - + +
14B MET* 4.8 3.4 - - - +
20B MET* 5.7 3.6 - - + -
21B ALA 3.5 8.9 + - - +
22B SER* 3.4 14.1 + - - +
23B ALA 3.2 0.4 - - - -
24B VAL* 1.3 81.5 - - - +
26B ALA* 1.3 56.9 + - - +
28B ARG* 3.3 14.1 + - - +
29B THR* 3.0 30.0 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.2 20.1 - - + -
22B SER 3.0 8.9 + - - +
23B ALA* 3.0 10.7 + - - +
25B ALA* 1.3 72.2 - - - +
27B ILE* 1.3 68.4 + - + +
29B THR* 2.4 28.0 + - - +
30B LEU* 3.0 18.2 + - + +
57B CYS* 5.9 5.4 - - + -
64B ALA 5.7 0.2 - - - +
65B VAL* 4.7 19.7 - - + +
68B GLY* 5.7 3.6 - - - -
72B PHE* 4.9 0.2 - - - -
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Residues in contact with ILE 27 (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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23B ALA* 2.9 23.7 + - + +
24B VAL* 3.2 18.1 + - + +
26B ALA* 1.3 76.1 - - - +
28B ARG* 1.3 57.8 + - - +
30B LEU 3.2 2.8 + - - -
31B LEU* 2.9 42.7 + - + +
68B GLY* 3.9 16.4 - - - -
71B LEU* 3.7 25.4 - - + -
72B PHE* 3.3 26.7 - - + -
100B PHE* 3.6 27.1 - - + -
101B LEU* 4.2 11.4 - - + -
104B ILE* 4.9 4.7 - - + -
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Residues in contact with ARG 28 (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 TYR* 3.7 7.2 - - + +
13B GLN* 3.2 33.6 + - - +
16B GLU* 5.6 0.6 + - - -
17B ASP* 4.8 9.3 + - - -
20B MET* 5.4 12.9 - - - +
24B VAL* 3.0 27.9 + - - +
25B ALA* 3.3 16.6 - - - +
27B ILE* 1.3 75.1 - - - +
29B THR* 1.3 60.8 + - - +
31B LEU* 3.6 10.6 - - + +
32B GLU* 2.9 31.8 + - + +
101B LEU* 3.4 44.4 - - + +
105B SER* 3.4 18.2 + - - -
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Residues in contact with THR 29 (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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5B GLU* 5.3 0.5 - - - +
6B LEU* 4.2 17.4 - - - +
9B TYR* 3.6 30.1 - - + +
10B PHE* 3.7 34.9 - - + +
13B GLN* 4.6 1.6 - - + -
25B ALA 3.0 15.2 + - - +
26B ALA* 2.4 30.3 + - - +
28B ARG* 1.3 76.6 - - - +
30B LEU* 1.3 68.6 + - - +
32B GLU* 3.3 2.9 + - - +
33B PHE* 2.9 26.7 + - - +
57B CYS* 4.6 5.1 - - - +
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Residues in contact with LEU 30 (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 LEU* 5.0 5.8 - - + -
26B ALA* 3.0 18.8 + - + +
29B THR* 1.3 85.9 + - - +
31B LEU* 1.3 63.9 + - - +
33B PHE* 3.6 19.7 - - + +
34B LEU* 4.0 8.8 - - - +
50B THR* 3.8 24.2 - - + +
54B GLU* 3.6 37.0 - - + -
57B CYS* 4.5 12.3 - - + -
68B GLY 5.2 1.6 - - - +
69B GLY* 5.7 0.4 - - - -
72B PHE* 3.5 54.0 - - + -
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Residues in contact with LEU 31 (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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27B ILE* 2.9 37.2 + - + +
28B ARG* 3.6 8.5 - - + +
29B THR 3.2 0.2 - - - -
30B LEU* 1.3 78.0 - - - +
32B GLU* 1.3 68.0 + - + +
33B PHE 3.2 0.2 - - - -
34B LEU* 3.3 28.7 + - - +
72B PHE* 3.7 19.5 - - + -
75B PHE* 4.8 4.5 - - + -
94B ILE* 5.7 2.6 - - - +
97B GLY* 3.3 42.0 - - - +
98B GLU* 4.1 8.7 - - - +
100B PHE* 5.0 1.3 - - + -
101B LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 32 (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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5B GLU* 5.0 0.7 - - - -
9B TYR* 3.4 34.1 - - + +
28B ARG* 2.9 17.3 + - + +
29B THR 3.6 2.2 - - - -
31B LEU* 1.3 81.4 - - + +
33B PHE* 1.3 54.7 + - - +
34B LEU* 3.1 7.5 + - - +
35B LYS* 2.5 43.5 + - - +
98B GLU* 5.7 1.0 - - - +
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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