Contacts of the helix formed by residues 6 - 20 (chain B) in PDB entry 1KOJ
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 ASN 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ALA 3.2 8.5 + - - +
3B LEU 2.9 15.7 + - - +
5B ARG* 1.3 77.5 - - - +
7B PRO* 1.3 71.3 - - - +
8B GLN* 2.7 47.3 + - - +
9B PHE* 3.1 10.1 + - + +
10B GLN* 3.1 23.9 + - - +
70B LEU* 3.5 9.1 - - - +
73B SER* 3.1 26.1 + - - +
74B ARG* 3.7 17.7 + - - -
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Residues in contact with PRO 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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5B ARG 3.6 6.9 - - - +
6B ASN* 1.3 86.7 - - - +
8B GLN* 1.3 82.0 + - - +
10B GLN* 3.3 9.4 + - + +
11B LYS* 3.0 28.4 + - - +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ASN* 2.7 18.9 + - - +
7B PRO* 1.3 91.8 - - - +
9B PHE* 1.3 61.2 + - - -
11B LYS* 3.4 11.7 + - + +
12B LEU* 3.1 23.2 + - - +
66B MET* 4.9 6.4 - - - +
69B ASP* 3.7 27.1 - - + +
70B LEU* 3.8 16.5 - - + +
73B SER* 3.1 32.0 + - - +
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Residues in contact with PHE 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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3B LEU* 3.5 57.7 - - + +
4B THR* 3.8 22.4 - - + -
6B ASN* 3.1 7.6 - - + +
8B GLN* 1.3 76.7 - - - +
10B GLN* 1.3 67.9 + - - +
12B LEU* 3.3 10.6 + - + +
13B GLN* 2.8 59.3 + - + +
70B LEU* 3.8 18.3 - - + +
324B ILE* 5.6 2.0 - - + -
328B ASN* 4.1 33.7 - - + -
329B CYS* 5.3 6.3 - - - -
372B HIS* 5.4 6.3 - - + -
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Residues in contact with GLN 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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4B THR* 2.7 36.0 + - - +
5B ARG 5.3 1.3 - - - -
6B ASN 3.1 17.2 + - - +
7B PRO* 3.6 11.4 - - + +
9B PHE* 1.3 87.4 - - - +
11B LYS* 1.3 56.9 + - - +
13B GLN* 3.1 32.0 + - - +
14B GLN* 2.8 32.3 + - - +
17B ARG* 4.9 0.3 + - - -
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Residues in contact with LYS 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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7B PRO 3.0 16.7 + - - +
8B GLN* 3.7 12.1 - - + +
10B GLN* 1.3 76.4 - - - +
12B LEU* 1.3 58.0 + - - +
14B GLN* 3.5 4.9 + - - +
15B TRP* 3.0 28.1 + - + +
65B HIS* 5.4 5.3 - - - -
66B MET* 4.1 29.7 - - + +
69B ASP* 5.2 6.7 + - - -
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Residues in contact with LEU 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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8B GLN 3.1 18.7 + - - +
9B PHE* 3.6 9.4 - - + +
11B LYS* 1.3 74.0 - - - +
13B GLN* 1.3 67.2 + - - +
15B TRP* 3.3 2.6 + - - +
16B HIS* 2.9 23.6 + - - +
63B VAL* 4.2 2.7 - - + +
66B MET* 3.6 41.9 - - + +
67B LEU* 3.5 34.8 - - + +
70B LEU* 4.7 14.8 - - + -
324B ILE* 5.6 3.4 - - + -
325B TRP* 3.6 32.2 - - + -
329B CYS* 4.2 10.1 - - - -
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Residues in contact with GLN 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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9B PHE* 2.8 47.0 + - + +
10B GLN* 3.1 31.3 + - - +
12B LEU* 1.3 77.1 - - - +
14B GLN* 1.3 56.8 + - - +
16B HIS* 3.3 2.6 + - - +
17B ARG* 2.9 77.4 + - + +
328B ASN 5.5 1.2 - - - +
329B CYS* 4.4 13.0 - - - -
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Residues in contact with GLN 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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10B GLN 2.8 20.6 + - - +
11B LYS* 3.8 6.1 - - - +
13B GLN* 1.3 74.6 - - - +
15B TRP* 1.3 61.1 + - - +
17B ARG* 3.4 23.4 + - - +
18B GLU* 3.0 56.3 + - - +
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Residues in contact with TRP 15 (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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11B LYS* 3.0 19.7 + - + +
12B LEU 3.5 4.5 - - - +
13B GLN 3.3 0.2 - - - -
14B GLN* 1.3 78.4 - - - +
16B HIS* 1.3 62.6 + - - +
18B GLU* 3.1 7.3 + - - -
19B HIS* 2.8 70.4 + + + -
20B GLY 4.4 3.4 - - - -
23B LEU* 4.1 26.9 - - + -
60B THR* 4.5 3.4 - - + -
62B GLU* 3.3 31.0 + - + +
63B VAL* 3.5 27.6 - - + -
66B MET* 3.4 27.3 - - + +
325B TRP* 4.1 13.7 - + - -
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Residues in contact with HIS 16 (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 LEU 2.9 17.0 + - - +
13B GLN 3.6 4.0 - - - +
15B TRP* 1.3 77.4 - - - +
17B ARG* 1.3 67.5 + - + +
18B GLU 2.9 7.4 + - - -
19B HIS 3.4 0.2 + - - -
20B GLY* 2.7 45.5 + - - +
21B SER 4.1 3.8 + - - -
325B TRP* 3.8 18.4 - - + -
329B CYS* 3.1 40.8 + - + +
330B PHE* 3.4 44.1 - + - -
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Residues in contact with ARG 17 (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 GLN* 4.9 1.0 + - - -
13B GLN* 2.9 58.1 + - + +
14B GLN* 3.4 22.1 + - - +
15B TRP 3.3 0.4 - - - -
16B HIS* 1.3 84.0 - - + +
18B GLU* 1.3 59.4 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 3.0 43.5 + - - +
15B TRP* 3.4 3.7 - - - +
16B HIS 2.9 0.4 - - - -
17B ARG* 1.3 78.6 - - - +
19B HIS* 1.3 92.1 + - + +
21B SER* 6.5 0.2 - - - -
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Residues in contact with HIS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 2.8 51.9 + + + +
18B GLU* 1.3 123.9 - - + +
20B GLY* 1.3 53.5 + - - +
21B SER* 3.2 4.2 - - - +
22B GLU* 2.5 52.7 + - + +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.4 2.2 - - - -
16B HIS* 2.7 52.1 + - - +
19B HIS* 1.3 72.0 - - - +
21B SER* 1.3 53.9 + - - +
22B GLU 2.6 20.3 + - - -
23B LEU* 3.3 20.6 + - - +
330B PHE* 4.5 7.6 - - - -
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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