Contacts of the strand formed by residues 7 - 15 (chain A) in PDB entry 1KQN
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 THR 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS* 1.3 70.2 - - - +
8A GLU* 1.3 75.7 + - - +
9A VAL* 3.6 9.4 + - + -
40A ARG 3.1 8.3 + - - -
41A TYR* 3.3 27.0 - - + -
42A THR 3.0 21.0 + - - -
148A VAL 6.1 0.2 - - - +
150A LYS* 4.6 23.3 - - + -
152A LYS* 5.9 0.9 - - - -
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Residues in contact with GLU 8 (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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6A LYS 3.6 6.6 + - - +
7A THR* 1.3 82.8 - - - +
9A VAL* 1.3 59.5 + - - +
42A THR* 3.2 18.2 - - - +
44A VAL* 3.8 25.9 - - + +
147A ALA 3.8 14.0 - - - +
148A VAL 5.6 0.2 - - - -
149A PRO* 3.5 28.2 - - + +
150A LYS 3.1 19.8 + - - -
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Residues in contact with VAL 9 (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 THR* 3.6 15.7 - - + +
8A GLU* 1.3 80.3 - - - +
10A VAL* 1.3 73.2 + - - +
11A LEU* 3.8 16.2 - - + -
35A MET* 4.5 5.2 - - + -
41A TYR* 3.7 25.8 - - + -
42A THR 2.9 10.1 + - - +
43A VAL* 3.5 12.7 - - + +
44A VAL* 2.8 29.6 + - - +
45A LYS 3.7 1.4 + - - +
150A LYS* 3.5 6.5 - - + +
152A LYS* 3.5 33.7 - - + -
184A ILE* 4.8 2.7 - - + -
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Residues in contact with VAL 10 (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 VAL* 1.3 82.9 - - - +
11A LEU* 1.3 68.3 + - - +
12A LEU* 3.6 1.0 + - + +
44A VAL* 3.9 16.4 - - + -
45A LYS* 3.4 21.3 - - + +
47A ILE* 4.0 27.8 - - + -
102A HIS* 6.4 0.4 - - + -
106A LEU* 3.8 35.0 - - + -
149A PRO* 4.0 6.1 - - + -
150A LYS 3.0 8.1 + - - +
151A VAL* 3.6 11.6 - - + -
152A LYS 2.9 27.4 + - - +
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Residues in contact with LEU 11 (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 VAL* 3.8 14.6 - - + -
10A VAL* 1.3 72.8 - - - +
12A LEU* 1.3 56.2 + - - +
13A ALA 4.0 0.2 - - - -
28A PHE* 3.7 10.5 - - + +
31A ALA* 3.7 28.3 - - + -
32A LYS 4.1 10.1 - - - +
35A MET* 4.7 0.4 - - + -
43A VAL* 4.1 26.5 - - + -
45A LYS 3.0 9.2 + - - +
46A GLY* 3.4 0.5 - - - -
47A ILE* 2.8 32.7 + - - +
79A TRP* 4.1 12.3 - - + -
152A LYS* 3.6 4.3 - - + +
154A LEU* 4.3 19.3 - - + -
184A ILE* 3.2 34.8 - - + -
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Residues in contact with LEU 12 (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 VAL* 3.6 2.0 + - + -
11A LEU* 1.3 72.1 - - - +
13A ALA* 1.3 61.7 + - - +
14A CYS* 4.2 12.6 - - - -
47A ILE* 3.5 32.5 - - + +
49A SER* 4.2 13.9 - - - -
98A VAL* 4.1 12.1 - - + -
99A LEU* 4.0 26.2 - - + -
102A HIS* 3.9 33.0 - - + +
151A VAL* 3.8 16.8 - - + -
152A LYS 2.8 15.5 + - - +
153A LEU* 3.4 9.7 - - + +
154A LEU* 2.8 24.3 + - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU 4.0 0.8 + - - -
12A LEU* 1.3 74.2 - - - +
14A CYS* 1.3 60.7 - - - +
17A PHE* 3.7 16.4 - - + -
27A LEU* 5.5 4.7 - - + -
28A PHE* 3.5 31.0 - - + -
47A ILE 2.9 9.5 + - - -
49A SER* 3.1 25.5 + - - -
154A LEU* 3.7 21.1 - - + +
777A NAD 6.0 3.6 - - - -
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Residues in contact with CYS 14 (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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12A LEU* 3.8 15.7 + - - -
13A ALA* 1.3 74.7 - - - +
15A GLY* 1.3 57.6 + - - +
17A PHE* 4.3 0.9 - - - -
49A SER* 3.8 6.1 - - - -
86A GLU* 3.6 20.6 - - - +
95A THR* 4.0 23.6 - - + +
98A VAL* 3.8 20.2 - - - -
153A LEU* 4.3 12.4 - - + +
154A LEU 4.5 1.7 + - - +
159A LEU* 4.2 12.5 - - + +
777A NAD 3.2 35.4 + - - +
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Residues in contact with GLY 15 (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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14A CYS* 1.3 75.5 - - - +
16A SER* 1.3 63.5 + - - -
17A PHE* 3.3 18.8 - - - -
49A SER 3.4 5.9 + - - -
50A PRO* 3.3 0.3 - - - +
51A VAL* 3.0 25.1 + - - -
777A NAD 3.3 30.5 + - - -
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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