Contacts of the strand formed by residues 16 - 24 (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 HIS 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASP* 3.1 3.5 + - - +
15A GLU* 1.3 103.1 + - + +
17A TYR* 1.3 83.1 + - + +
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Residues in contact with TYR 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 PHE* 3.0 7.0 - - - +
14A ASP* 2.9 36.3 + - - +
15A GLU 4.1 0.2 - - - -
16A HIS* 1.3 95.1 - - + +
18A GLU* 1.3 66.9 + - - +
19A TYR* 3.8 30.0 - + + -
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Residues in contact with GLU 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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11A LYS* 3.7 32.1 + - + +
12A TYR 3.4 10.3 - - - +
13A PHE* 4.0 10.5 - - + +
17A TYR* 1.3 83.6 - - - +
19A TYR* 1.3 67.4 + - - +
54A TRP* 3.7 31.1 - - + -
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Residues in contact with TYR 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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11A LYS* 3.2 10.2 - - - +
12A TYR* 2.7 73.9 + + + +
13A PHE* 4.1 2.0 - - - -
14A ASP* 2.7 41.8 + - + -
17A TYR* 3.8 31.2 - + + +
18A GLU* 1.3 77.9 - - - +
20A ARG* 1.3 61.5 + - - +
54A TRP* 3.8 6.6 - - - -
57A TYR* 3.5 42.6 - + + -
58C MET* 4.8 7.1 - - - -
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Residues in contact with ARG 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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8A TYR* 4.2 17.1 - - - +
9A SER* 3.2 27.6 + - - +
10A ASP* 4.4 2.7 - - - +
11A LYS* 3.4 22.5 - - + +
12A TYR* 4.5 2.4 + - - -
19A TYR* 1.3 77.5 - - - +
21A HIS* 1.3 81.5 + - - +
22A VAL* 4.0 10.0 - - - +
50A GLN* 3.4 26.0 + - - +
54A TRP* 3.5 34.2 - - + +
57A TYR* 5.6 5.6 - - - -
300A SO4 2.8 41.7 + - - -
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Residues in contact with HIS 21 (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* 2.9 40.4 + - - +
12A TYR* 3.2 33.7 + + - -
20A ARG* 1.3 84.6 - - - +
22A VAL* 1.3 62.0 + - - +
23A MET* 3.6 20.4 - - + +
57A TYR* 5.6 3.5 + - - -
60A HIS* 5.1 18.7 + + - -
61C GLU* 4.3 15.8 - - + +
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Residues in contact with VAL 22 (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* 3.4 30.1 - - + -
7A TYR 3.4 3.4 - - - -
8A TYR* 3.8 23.6 - - + -
20A ARG* 4.0 11.2 - - - +
21A HIS* 1.3 77.6 - - - +
23A MET* 1.3 64.0 + - - +
24A LEU* 3.7 19.4 + - + +
48A VAL* 4.3 15.7 - - + -
50A GLN* 4.1 10.3 - - - +
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Residues in contact with MET 23 (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 4.2 0.3 - - - +
6A ILE* 3.5 8.1 - - - +
7A TYR* 2.9 74.2 + - + +
9A SER* 4.6 3.8 - - - -
21A HIS* 3.6 33.0 - - + +
22A VAL* 1.3 77.9 - - - +
24A LEU* 1.3 63.4 + - - +
25A PRO* 4.1 0.5 - - - +
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Residues in contact with LEU 24 (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* 4.2 18.8 - - + -
22A VAL* 3.7 29.0 + - + +
23A MET* 1.3 76.1 - - - +
25A PRO* 1.3 70.3 - - - +
26A ARG 3.6 1.2 + - - -
28A LEU* 4.1 19.5 - - + +
29A SER* 3.7 19.2 + - - +
32A VAL* 3.6 30.7 - - + -
38A MET* 6.1 0.4 - - + -
46A LEU* 4.2 7.4 - - + -
48A VAL* 4.5 9.0 - - + -
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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