Contacts of the helix formed by residues 9 - 20 (chain A) in PDB entry 4KPD
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TYR* 1.3 82.0 + - + +
11A ALA* 3.5 7.1 - - - +
12A GLN* 3.8 14.1 - - + +
13A GLU* 3.2 31.7 + - + +
66A VAL* 3.7 36.5 - - + +
69A ARG* 6.5 0.2 - - - -
70A GLU* 4.9 7.2 - - - +
343A GLY* 5.2 7.4 - - - -
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Residues in contact with TYR 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 91.4 - - + +
11A ALA* 1.4 57.0 + - - +
13A GLU* 3.3 3.5 + - - -
14A LYS* 3.0 30.6 + - - +
59A ASN* 3.7 12.8 - - - -
62A LEU* 3.6 28.3 - - + +
63A THR* 2.7 45.1 + - - +
66A VAL* 4.6 14.7 - - + +
340A VAL 4.9 2.8 + - - -
343A GLY* 3.5 32.1 - - - -
344A LEU* 3.4 23.3 + - + +
347A LYS* 3.8 39.3 - - + -
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Residues in contact with ALA 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 4.3 4.2 - - - +
10A TYR* 1.4 78.2 - - - +
12A GLN* 1.3 60.9 + - - +
14A LYS* 3.8 17.5 - - - +
15A GLN* 4.9 3.8 + - - +
347A LYS* 5.1 4.2 - - - +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.7 16.4 + - + +
11A ALA* 1.3 81.3 - - - +
13A GLU* 1.3 60.6 + - + +
14A LYS 3.4 0.9 + - - -
15A GLN* 4.2 5.7 + - - +
16A ASP* 3.1 16.5 - - - +
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Residues in contact with GLU 13 (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* 3.2 23.8 + - + +
10A TYR 3.3 1.3 + - - +
12A GLN* 1.3 79.2 - - + +
14A LYS* 1.4 58.0 + - - +
15A GLN 3.5 0.7 - - - -
16A ASP* 3.4 21.7 + - - +
17A PHE* 3.0 30.7 + - - +
62A LEU* 3.7 16.2 - - + -
65A VAL* 3.5 23.0 - - - +
66A VAL* 4.4 11.7 - - + +
69A ARG* 2.7 41.9 + - - -
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Residues in contact with LYS 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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10A TYR 3.0 15.5 + - - +
11A ALA* 3.8 14.6 - - - +
12A GLN 3.3 1.2 - - - -
13A GLU* 1.4 74.8 - - - +
15A GLN* 1.4 69.7 + - + +
17A PHE* 3.3 3.3 + - - +
18A VAL* 3.0 35.4 + - + +
56A GLY 4.4 9.3 + - - -
57A LYS* 4.3 13.3 + - - +
58A TYR* 3.8 33.7 - - + -
62A LEU* 4.0 15.3 - - + -
347A LYS* 6.6 0.2 - - - -
353A LYS* 5.8 4.9 - - - +
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Residues in contact with GLN 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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11A ALA 5.5 3.4 - - - +
12A GLN 4.2 5.1 + - - +
13A GLU 3.5 0.2 - - - -
14A LYS* 1.4 89.5 - - + +
16A ASP* 1.3 60.7 + - - +
18A VAL* 3.5 8.6 + - - +
19A GLN* 3.0 46.4 + - - +
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Residues in contact with ASP 16 (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 GLN 3.1 22.4 - - - +
13A GLU* 3.6 20.2 - - - +
14A LYS 3.3 0.2 - - - -
15A GLN* 1.3 77.6 - - - +
17A PHE* 1.4 58.2 + - - +
19A GLN* 3.4 23.1 + - - +
20A HIS* 3.0 28.5 + - - +
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Residues in contact with PHE 17 (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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13A GLU* 3.0 18.4 + - - +
14A LYS 3.3 4.2 + - - +
16A ASP* 1.4 74.3 - - - +
18A VAL* 1.3 63.9 + - + +
20A HIS* 3.3 14.2 + - - +
58A TYR* 3.9 31.9 - + + -
61A GLY* 3.6 31.6 - - - -
62A LEU* 3.7 13.9 - - + -
65A VAL* 3.9 20.4 - - + -
86A TRP* 3.7 16.4 - - + -
89A GLY* 3.8 1.1 - - - -
90A TRP* 2.9 76.7 + + - -
93A GLU* 4.0 7.9 - - + -
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Residues in contact with VAL 18 (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 LYS* 3.0 25.0 + - + +
15A GLN* 4.1 10.1 - - - +
17A PHE* 1.3 72.9 - - + +
19A GLN* 1.3 64.7 + - + +
20A HIS 3.1 0.2 - - - -
21A PHE* 3.0 20.3 + - + +
22A SER 4.5 0.5 + - - -
54A ILE* 4.7 16.2 - - + -
58A TYR* 3.5 43.1 - - + +
90A TRP* 4.1 6.7 - - + -
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Residues in contact with GLN 19 (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 GLN* 3.0 31.3 + - - +
16A ASP* 3.5 14.5 - - - +
17A PHE 3.3 0.4 - - - -
18A VAL* 1.3 74.3 - - - +
20A HIS* 1.4 62.3 - - + +
21A PHE 3.6 0.5 + - - -
22A SER* 4.0 14.9 + - - -
23A GLN* 4.0 6.1 - - - +
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Residues in contact with HIS 20 (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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16A ASP* 3.0 30.5 + - - +
17A PHE* 3.3 11.9 + - - +
18A VAL 3.1 1.2 - - - -
19A GLN* 1.4 77.9 - - + +
21A PHE* 1.3 62.9 + - - +
22A SER 3.3 1.3 - - - -
23A GLN* 3.0 39.8 + - - +
24A ILE* 3.3 13.7 + - - +
86A TRP* 3.1 68.1 + + + -
90A TRP* 4.2 5.6 - - - +
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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