Contacts of the strand formed by residues 54 - 60 (chain C) 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 TRP 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LYS* 4.0 30.7 - - + -
18C GLU* 3.6 51.6 - - + -
19C TYR* 3.8 15.9 - - - -
20C ARG* 3.9 27.1 - - + +
40C GLU* 4.7 4.1 + - - +
43C TRP* 3.4 22.9 + - + -
50C GLN* 3.6 33.0 - - + +
51C SER* 3.3 40.6 + - - -
52C LEU 4.3 3.3 + - - -
53C GLY* 1.3 76.7 - - - +
55C VAL* 1.3 65.2 + - - +
302C SO4 3.8 8.3 + - - -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 3.9 21.5 - - - +
43C TRP* 5.1 0.7 - - - +
53C GLY 3.7 10.2 + - - +
54C TRP* 1.3 83.3 - - - +
56C HIS* 1.3 68.1 + - - +
57C TYR* 3.1 23.8 + - + +
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Residues in contact with HIS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 5.1 0.2 - - - +
32C VAL* 5.1 4.0 - - + +
36C HIS 4.9 0.6 + - - -
37C LEU* 3.5 31.8 - - + +
38C MET* 3.1 71.7 + - + +
43C TRP* 4.1 18.3 - - + +
55C VAL* 1.3 73.5 - - - +
57C TYR* 1.3 59.8 + - - +
58C MET 3.6 22.0 + - - -
59C ILE* 3.8 20.0 - - + +
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Residues in contact with TYR 57 (chain C).
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* 3.2 27.3 - - + +
15A GLU* 3.5 30.6 + - - +
12C TYR* 4.6 6.6 + - - -
19C TYR* 3.4 39.6 - + + -
20C ARG 5.8 4.5 - - - -
21C HIS* 6.1 0.5 - - - -
37C LEU* 3.8 8.1 - - - -
55C VAL* 3.1 20.7 + - + +
56C HIS* 1.3 74.4 + - - +
58C MET* 1.3 94.0 + - + +
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Residues in contact with MET 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 4.8 5.8 - - + -
13A PHE 3.6 12.1 - - - +
14A ASP* 3.9 17.3 - - + +
19A TYR* 4.8 10.5 - - - -
37C LEU* 3.7 6.4 - - - +
56C HIS* 3.6 15.4 + - - -
57C TYR* 1.3 117.9 - - + +
59C ILE* 1.3 77.7 + - - +
60C HIS* 3.9 1.9 + - - -
61C GLU* 4.1 17.7 - - - +
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Residues in contact with ILE 59 (chain C).
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 5.5 1.1 - - - +
12A TYR* 3.6 16.9 - - + -
13A PHE* 2.9 57.8 + - + +
32C VAL* 5.4 4.7 - - + -
33C PRO 4.6 10.5 - - - +
34C LYS* 5.3 2.2 - - - +
36C HIS 4.6 6.7 - - - +
37C LEU* 4.2 3.8 - - + -
56C HIS* 3.8 26.7 - - + +
58C MET* 1.3 88.0 - - - +
60C HIS* 1.3 76.0 + - - +
61C GLU* 3.3 4.7 - - - +
62C PRO* 5.4 4.3 - - + -
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 4.3 0.9 - - - -
21C HIS* 6.1 4.6 + + - -
58C MET* 3.9 3.5 + - - -
59C ILE* 1.3 86.0 - - - +
61C GLU* 1.3 114.2 + - + +
62C PRO* 3.1 12.9 - - + +
63C GLU* 3.4 28.1 + - - +
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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