Contacts of the strand formed by residues 5 - 15 (chain A) in PDB entry 1CKS
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 GLN 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 1.3 73.8 - - - +
6A ILE* 1.3 60.2 + - - +
7A TYR 4.1 1.2 + - - -
23A MET 4.2 0.2 - - - +
25A PRO* 2.9 41.6 - - + +
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Residues in contact with ILE 6 (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 LYS* 3.3 17.2 + - + +
5A GLN* 1.3 77.1 - - - +
7A TYR* 1.3 60.7 + - - +
8A TYR* 3.6 35.0 + - + +
22A VAL* 3.4 32.1 - - + -
23A MET 3.5 6.1 - - - +
24A LEU* 4.2 10.8 - - + -
25A PRO* 4.4 1.8 - - + -
28A LEU* 3.7 31.2 - - + -
47A GLY 3.5 32.1 - - - +
48A VAL* 4.2 4.3 - - + +
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Residues in contact with TYR 7 (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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5A GLN 4.1 1.0 + - - -
6A ILE* 1.3 73.1 - - - +
8A TYR* 1.3 74.9 + - - +
9A SER* 4.0 12.9 - - - -
10A ASP* 5.5 2.9 + - - -
22A VAL* 3.4 5.2 - - - -
23A MET* 2.9 76.3 + - + +
64C PRO* 4.3 29.5 - - + +
65C HIS 5.1 2.1 + - - -
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Residues in contact with TYR 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 ILE* 3.6 35.5 - - + +
7A TYR* 1.3 85.8 + - - +
9A SER* 1.3 63.3 + - - +
10A ASP* 5.3 0.7 - - - +
20A ARG* 4.2 22.0 - - - +
21A HIS 4.1 2.0 - - - -
22A VAL* 3.8 15.0 - - + -
47A GLY 3.7 4.2 + - - -
48A VAL* 3.5 29.3 - - + -
49A GLN* 2.8 43.1 + - + +
50A GLN* 4.7 3.6 - - + -
300A SO4 5.7 0.4 - - - -
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Residues in contact with SER 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 TYR* 3.8 19.7 + - - -
8A TYR* 1.3 75.8 - - - +
10A ASP* 1.3 73.6 + - - +
12A TYR* 4.9 1.7 - - - -
20A ARG* 3.2 20.4 + - - -
21A HIS* 2.9 55.0 + - - +
23A MET* 4.9 4.0 - - - -
62C PRO* 5.3 7.9 - - - -
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Residues in contact with ASP 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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7A TYR* 5.5 3.6 + - - -
8A TYR 5.3 0.9 - - - +
9A SER* 1.3 90.4 + - - +
11A LYS* 1.3 67.9 + - - +
12A TYR* 3.9 9.4 + - - -
19A TYR 4.3 0.9 - - - +
20A ARG* 4.4 0.8 - - - +
62C PRO* 4.4 24.3 + - + +
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Residues in contact with LYS 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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10A ASP* 1.3 80.0 - - - +
12A TYR* 1.3 61.4 + - - +
13A PHE* 5.4 3.8 - - + -
18A GLU* 3.7 29.8 + - + +
19A TYR 3.2 14.4 - - - +
20A ARG* 3.4 31.9 - - - +
54A TRP* 3.9 17.6 - - + -
300A SO4 3.5 25.2 + - - -
59C ILE* 5.5 1.4 - - - +
62C PRO* 4.5 7.0 - - - +
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Residues in contact with TYR 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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9A SER* 4.9 0.7 - - - -
10A ASP 4.0 7.6 - - - -
11A LYS* 1.3 77.6 - - - +
13A PHE* 1.3 64.2 + - - +
18A GLU* 3.4 4.1 - - - +
19A TYR* 2.7 76.2 + + + +
20A ARG* 4.3 4.7 + - - -
21A HIS* 3.2 36.5 + + - -
57A TYR* 4.7 4.7 + - - -
58C MET* 4.8 6.7 - - - -
59C ILE* 3.6 23.6 - - + +
60C HIS 4.1 10.3 - - - +
61C GLU* 3.4 48.7 - - + +
62C PRO* 4.2 3.6 - - + -
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Residues in contact with PHE 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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11A LYS* 5.4 2.5 - - + -
12A TYR* 1.3 81.3 - - - +
14A ASP* 1.3 72.9 + - - +
17A TYR 3.0 16.2 - - - +
18A GLU* 4.0 12.8 - - + -
19A TYR* 4.1 4.7 - - - -
34C LYS 3.4 19.3 - - - -
35C THR* 3.7 6.7 - - - -
36C HIS* 3.6 26.0 - - - -
37C LEU* 3.9 24.7 - - + -
58C MET* 3.6 3.2 - - - +
59C ILE* 2.9 52.9 + - + +
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Residues in contact with ASP 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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13A PHE* 1.3 89.2 - - - +
15A GLU* 1.3 61.8 + - - +
16A HIS* 3.1 6.2 + - - -
17A TYR* 2.9 45.1 + - - +
19A TYR* 2.7 29.8 + - + -
37C LEU* 3.9 6.4 - - - +
57C TYR* 3.2 25.1 - - + +
58C MET* 3.9 18.6 - - + +
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Residues in contact with GLU 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 ASP* 1.3 78.1 + - - +
16A HIS* 1.3 87.3 + - + +
37C LEU* 3.8 16.3 - - + +
55C VAL* 3.9 20.3 - - - +
56C HIS 5.1 0.2 - - - +
57C TYR* 3.8 26.9 - - - +
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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