Contacts of the strand formed by residues 7 - 15 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LYS* 1.3 71.1 - - - +
8F GLU* 1.3 75.7 + - - +
9F VAL* 3.5 2.0 + - + -
40F ARG 3.2 7.9 + - - -
41F TYR* 3.4 30.2 - - + +
42F THR* 3.1 20.9 + - - -
148F VAL 6.0 0.2 - - - +
150F LYS* 4.2 31.0 + - + +
152F LYS* 6.1 0.4 - - - +
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Residues in contact with GLU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS 3.7 6.7 + - - +
7F THR* 1.3 79.9 - - - +
9F VAL* 1.3 54.1 + - - +
42F THR* 3.4 15.9 - - - +
44F VAL* 3.8 22.4 - - + +
148F VAL 5.4 0.6 - - - -
149F PRO* 3.1 34.9 - - + +
150F LYS 2.7 30.1 + - - -
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F THR* 4.4 4.0 - - + +
8F GLU* 1.3 76.2 - - - +
10F VAL* 1.3 70.2 + - - +
11F LEU* 4.3 8.5 - - + -
35F MET* 4.6 9.0 - - + -
41F TYR* 4.5 15.9 - - + -
42F THR 3.0 11.1 + - - +
43F VAL* 3.4 37.0 - - + +
44F VAL* 2.8 32.1 + - - +
45F LYS 3.7 0.7 + - - -
150F LYS* 3.3 6.5 - - + +
152F LYS* 3.4 38.4 - - + -
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Residues in contact with VAL 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 1.3 72.2 - - - +
11F LEU* 1.3 67.5 + - - +
12F LEU 3.6 0.3 + - - -
44F VAL* 3.5 24.9 - - + -
45F LYS* 3.4 20.4 - - + +
47F ILE* 3.8 33.2 - - + -
102F HIS* 6.2 0.2 - - + -
106F LEU* 4.0 32.1 - - + -
149F PRO* 4.3 4.7 - - + -
150F LYS 2.8 11.8 + - - +
151F VAL* 3.3 11.6 - - + -
152F LYS* 2.9 26.0 + - - +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.3 13.7 - - + -
10F VAL* 1.3 75.8 - - - +
12F LEU* 1.3 60.7 + - - +
13F ALA 4.0 0.4 - - - -
28F PHE* 3.8 4.9 - - + -
31F ALA* 3.8 25.6 - - + -
32F LYS 4.2 3.6 - - - +
35F MET* 4.9 1.3 - - + -
43F VAL* 3.7 28.5 - - + -
45F LYS 3.0 8.0 + - - +
46F GLY* 3.5 0.2 - - - -
47F ILE* 2.8 29.5 + - - +
79F TRP* 3.9 18.2 - - + -
152F LYS* 3.5 6.1 - - + +
154F LEU* 4.1 19.3 - - + -
184F ILE* 3.4 33.9 - - + -
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL 3.6 0.6 + - - -
11F LEU* 1.3 73.3 - - - +
13F ALA* 1.3 58.2 + - - +
14F CYS* 4.0 20.2 - - - -
47F ILE* 3.7 31.4 - - + +
49F SER* 4.0 18.4 - - - -
98F VAL* 4.0 21.1 - - + +
99F LEU* 3.7 26.5 - - + -
102F HIS* 4.1 15.0 - - + +
151F VAL* 3.7 19.5 - - + -
152F LYS 2.8 11.2 + - - +
153F LEU* 3.3 9.8 - - + +
154F LEU* 2.8 26.7 + - - +
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Residues in contact with ALA 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU 4.0 0.6 + - - -
12F LEU* 1.3 74.2 - - - +
14F CYS* 1.3 62.4 + - - +
17F PHE* 3.9 14.0 - - + -
27F LEU* 5.9 3.4 - - + -
28F PHE* 3.3 33.7 - - + -
47F ILE 3.0 8.5 + - - -
48F ILE* 3.8 0.5 - - - -
49F SER* 3.0 26.0 + - - +
154F LEU* 3.6 21.8 - - + +
782F NAD 6.1 2.0 - - - -
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Residues in contact with CYS 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 3.9 17.7 + - - -
13F ALA* 1.3 73.8 - - - +
15F GLY* 1.3 56.7 + - - +
17F PHE* 4.0 1.3 - - - -
49F SER* 3.6 6.7 - - - -
86F GLU* 3.6 20.9 - - - +
95F THR* 4.1 23.3 - - + +
98F VAL* 3.6 28.0 - - - -
153F LEU* 4.2 7.8 - - + +
154F LEU 4.3 1.2 + - - +
159F LEU* 4.2 13.8 - - + +
782F NAD 3.2 31.6 + - - +
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Residues in contact with GLY 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F CYS* 1.3 74.0 - - - +
16F SER* 1.3 63.2 + - - -
17F PHE* 3.3 24.4 - - - -
49F SER 3.5 2.0 + - - -
50F PRO* 3.3 0.3 - - - +
51F VAL* 2.8 25.0 + - - -
782F NAD 3.1 31.8 + - - -
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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