Contacts of the strand formed by residues 6 - 14 (chain B) in PDB entry 4K71
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 SER 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LEU* 1.3 81.6 - - - +
7B LEU* 1.3 59.9 + - - +
8B LEU* 3.8 24.2 - - - +
29B TRP 3.5 2.6 - - - +
30B LEU* 3.5 2.8 - - - -
31B GLY* 3.0 31.2 + - - -
96B CYS 3.2 15.9 - - - -
97B GLU* 4.0 15.7 - - - -
163B LEU* 4.0 7.4 - - - -
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Residues in contact with LEU 7 (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 SER* 1.3 72.7 - - - +
8B LEU* 1.3 61.2 + - - +
9B TYR* 4.1 15.7 - - + -
29B TRP 3.2 8.1 - - - +
30B LEU* 4.2 9.6 - - + -
35B TYR* 3.1 44.4 - - + +
95B GLY* 3.2 5.0 - - - -
96B CYS 2.9 29.7 + - - +
159B CYS* 3.4 38.8 - - - +
162B ARG* 3.6 22.4 - - + -
163B LEU* 3.8 17.6 - - + +
166B HIS* 5.2 0.7 - - + -
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Residues in contact with LEU 8 (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 SER* 3.8 22.4 - - - +
7B LEU* 1.3 80.6 - - - +
9B TYR* 1.3 63.0 + - - +
10B HIS* 4.2 9.2 - - + -
28B GLY* 3.6 0.9 - - - -
29B TRP* 2.8 44.5 + - + +
93B LEU* 4.2 32.8 - - + -
94B LEU 3.7 3.6 - - - -
95B GLY* 3.8 22.7 - - - +
96B CYS* 4.2 2.2 - - - +
107B THR* 4.3 13.0 - - + -
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Residues in contact with TYR 9 (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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7B LEU* 4.1 19.5 - - + +
8B LEU* 1.3 76.0 - - - +
10B HIS* 1.3 60.4 + - - +
11B LEU* 3.5 15.0 - - + +
26B VAL* 4.1 19.7 - - + -
27B SER 3.6 3.1 - - - -
28B GLY* 4.4 7.0 - - - -
35B TYR* 3.1 18.9 + - - -
36B LEU* 4.1 9.2 - - + -
64B GLU* 2.7 29.4 + - - -
68B LEU* 4.2 11.7 - - + -
92B GLY 3.5 5.7 - - - +
93B LEU* 3.5 4.5 - - - +
94B LEU* 2.8 41.8 + - + +
95B GLY* 4.8 1.1 - - - -
154B PHE* 3.5 31.0 - + + -
159B CYS* 4.9 7.2 - - + -
162B ARG* 3.3 21.2 + - - -
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Residues in contact with HIS 10 (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 LEU* 4.0 13.2 + - + -
9B TYR* 1.3 71.9 - - - +
11B LEU* 1.3 61.5 + - - +
12B THR* 4.2 0.5 + - - -
25B TRP* 3.8 1.7 - - - +
26B VAL* 3.2 5.5 - - - -
27B SER* 2.8 40.6 + - - +
29B TRP* 3.7 25.3 - + + -
92B GLY 3.7 4.7 - - - -
93B LEU* 3.3 24.5 - - + +
55C SER* 3.4 15.9 - - - +
56C PHE* 3.0 53.3 + + + -
57C SER* 5.4 1.6 - - - -
63C TYR* 5.5 0.6 + - - -
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Residues in contact with LEU 11 (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* 3.5 21.3 - - + +
10B HIS* 1.3 72.4 - - - +
12B THR* 1.3 64.7 + - - +
24B PHE* 4.0 16.8 - - + -
25B TRP 3.7 4.3 - - - -
26B VAL* 4.0 14.6 - - + -
68B LEU* 4.7 7.6 - - + -
71B LYS* 3.7 31.2 - - + -
75B PHE* 3.7 21.5 - - + -
91B GLN* 3.2 4.5 - - - -
92B GLY 2.9 46.7 + - - +
94B LEU* 3.5 32.1 - - + -
154B PHE* 6.2 0.4 - - + -
56C PHE* 3.5 2.9 - - - -
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Residues in contact with THR 12 (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 HIS 4.8 0.3 + - - -
11B LEU* 1.3 77.7 + - - +
13B ALA* 1.3 65.1 + - - +
14B VAL* 4.4 0.7 - - + -
24B PHE* 3.2 10.4 - - - -
25B TRP* 3.0 74.3 + - + -
75B PHE* 4.5 0.4 - - - -
89B THR* 4.0 14.6 - - + -
90B LEU 3.4 4.5 - - - +
91B GLN* 4.0 1.7 - - + +
56C PHE* 3.3 22.5 - - - -
62C PHE* 3.9 21.9 - - + -
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Residues in contact with ALA 13 (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 THR* 1.3 74.5 - - - +
14B VAL* 1.3 63.6 + - - +
23B ALA 3.2 8.7 - - - +
24B PHE* 4.1 4.3 - - + -
75B PHE* 3.7 34.5 - - + +
76B LEU* 4.3 4.7 - - + -
79B PHE* 3.5 21.1 - - + -
89B THR* 3.4 4.7 - - - +
90B LEU* 2.9 33.3 + - + +
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Residues in contact with VAL 14 (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 THR* 4.4 0.2 - - + -
13B ALA* 1.3 79.1 - - - +
15B SER* 1.3 62.3 + - - +
16B SER 4.3 3.8 - - - +
17B PRO* 3.8 37.2 - - + +
22B PRO 4.4 0.2 - - - +
23B ALA* 2.9 25.3 + - - +
25B TRP* 4.1 19.1 - - + -
76B LEU* 4.6 1.0 - - - +
79B PHE* 3.5 9.0 - - - -
88B TYR 3.3 5.8 - - - +
89B THR* 3.9 18.8 - - + +
33C SER* 3.8 22.2 - - - +
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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