Contacts of the strand formed by residues 22 - 32 (chain A) in PDB entry 3KNB
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 VAL 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.4 2.7 - - - +
20A GLY 5.6 0.2 - - - +
21A LYS* 1.3 78.4 - - - +
23A LEU* 1.3 65.9 + - - +
24A THR* 4.3 4.7 - - - +
66A ILE* 3.9 13.5 - - + -
67A ILE 3.4 9.4 - - - +
68A MET* 3.8 35.2 - - + -
69A ASP 4.3 2.9 - - - +
13B PRO* 3.8 35.2 - - + +
92B ALA* 3.1 9.4 + - + +
93B GLY* 3.1 1.9 - - - -
94B GLU 2.9 27.4 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.8 17.5 - - + -
16A SER 4.2 8.5 - - - +
17A ILE* 3.9 22.0 - - + -
21A LYS 4.0 1.0 + - - -
22A VAL* 1.3 74.5 - - - +
24A THR* 1.3 71.0 + - - +
25A VAL* 4.4 1.8 - - + -
65A LEU 3.8 0.7 - - - +
66A ILE* 3.3 4.5 - - - +
67A ILE* 2.8 47.3 + - + +
70A VAL* 4.2 8.1 - - + -
95A ILE* 3.6 37.7 - - + -
94B GLU 3.5 4.5 - - - +
96B TYR* 3.6 36.3 - - + -
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.3 6.1 - - - +
23A LEU* 1.3 77.0 + - - +
25A VAL* 1.3 73.6 + - - +
26A ALA 4.7 1.1 - - - +
64A THR* 3.6 27.4 - - + -
65A LEU 3.4 4.0 - - - +
66A ILE* 3.8 17.8 - - + +
13B PRO* 5.6 1.0 - - - +
14B PRO 3.9 11.2 + - - +
15B CYS* 5.3 5.7 - - + +
16B PHE* 5.2 7.6 - - + -
94B GLU 2.9 12.3 + - - -
95B ALA* 3.2 15.9 - - + -
96B TYR* 2.9 28.2 + - - -
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 27.4 - - + -
12A PRO* 4.5 9.0 - - + -
15A ILE* 3.1 35.9 - - + -
23A LEU* 4.4 7.0 - - + -
24A THR* 1.3 81.5 - - - +
26A ALA* 1.3 64.6 + - - +
39A TRP* 4.6 10.4 - - + -
63A THR 3.8 1.4 - - - +
64A THR* 3.3 2.1 - - - -
65A LEU* 2.9 49.7 + - + +
93A VAL* 5.2 4.0 - - + -
95A ILE* 5.0 4.9 - - + -
96B TYR* 3.5 12.3 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 5.2 0.5 - - - +
11A LEU* 5.2 1.2 - - - +
12A PRO* 5.6 0.3 - - - +
24A THR* 4.3 1.0 - - + +
25A VAL* 1.3 76.9 - - - +
27A CYS* 1.3 61.0 + - - +
62A LEU* 4.5 4.7 - - + -
63A THR 3.4 4.0 - - - -
64A THR* 3.8 17.7 - - + +
16B PHE* 4.0 18.2 - - + -
19B PHE* 2.8 43.1 - - + -
96B TYR 3.1 12.7 + - - +
97B ALA* 3.8 4.3 - - - -
98B ALA 4.4 1.9 + - - -
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Residues in contact with CYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.4 33.0 - - - -
10A ALA 3.4 20.0 - - - -
11A LEU* 3.9 20.6 - - + -
25A VAL 4.2 0.2 + - - -
26A ALA* 1.3 75.6 - - - +
28A ALA* 1.3 69.2 + - - +
29A PHE* 4.0 0.3 - - - -
39A TRP* 4.9 2.9 - - + -
62A LEU* 3.5 4.9 - - - +
63A THR* 2.8 42.0 + - + +
80A LEU* 3.8 19.3 - - + -
19B PHE* 3.9 2.0 - - - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU* 2.9 43.2 + - + +
10A ALA 5.0 0.6 + - - -
27A CYS* 1.3 81.2 - - - +
29A PHE* 1.3 63.9 + - - +
61A ASP 3.3 6.5 - - - -
62A LEU* 3.8 1.3 - - - -
19B PHE* 3.7 24.3 - - + -
21B ARG* 3.3 29.8 - - - +
22B PRO* 5.2 2.0 - - + -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS 3.2 15.5 - - - +
8A ILE* 4.3 1.6 - - + -
9A GLU* 3.8 3.2 - - - +
27A CYS 4.0 6.5 - - - -
28A ALA* 1.3 80.1 - - - +
30A THR* 1.3 69.7 + - - +
34A THR* 4.3 2.9 - - + -
35A PRO* 4.0 33.0 - - + -
37A VAL* 3.9 24.2 - - + -
59A THR 3.4 22.4 - - - -
60A ASP 3.4 18.8 - - - +
61A ASP* 3.1 23.8 + - - +
62A LEU 3.4 30.1 - - - -
63A THR* 3.7 9.0 - - + -
80A LEU* 5.6 1.3 - - + -
82A LEU* 3.4 21.3 - - + -
21B ARG* 4.8 1.2 + - - -
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 5.8 2.3 - - - +
5A PRO 4.8 1.3 + - - -
6A PRO* 3.2 4.0 - - - +
7A LYS* 2.9 44.6 + - - +
9A GLU* 3.6 22.0 - - - +
29A PHE* 1.3 80.5 - - - +
31A GLY* 1.3 59.4 + - - +
35A PRO* 3.6 10.6 - - - +
60A ASP 5.6 1.3 - - - -
61A ASP* 5.7 1.3 - - + -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.7 13.4 - - - +
5A PRO 4.0 7.2 - - - -
6A PRO* 4.1 0.7 - - - -
30A THR* 1.3 78.8 - - - +
32A GLU* 1.3 69.7 + - - +
33A PRO 3.3 14.8 - - - +
34A THR* 3.6 7.6 + - - -
35A PRO* 3.7 12.1 - - - +
60A ASP 5.6 0.9 - - - +
84A ASN* 4.2 0.2 - - - -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 3.5 23.3 - - + +
3A GLY* 3.4 2.6 - - - -
4A ILE* 2.9 42.0 + - + +
31A GLY* 1.3 82.3 - - - +
33A PRO* 1.3 71.7 + - + +
34A THR* 4.2 7.7 + - - -
84A ASN* 3.5 1.8 - - - -
86A PHE* 3.3 6.2 - - - -
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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