Contacts of the strand formed by residues 9 - 14 (chain A) in PDB entry 5KFP
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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7A ARG* 3.9 31.4 - - + +
8A VAL* 1.3 83.0 - - - +
10A ALA* 1.3 73.7 + - - +
118A TYR* 4.3 1.1 - - + -
119A VAL 3.4 7.4 - - - +
120A ASP* 5.0 2.9 - - - -
216A ILE* 3.6 1.6 - - - +
217A SER 2.9 31.5 + - - -
218A HIS 4.1 4.3 - - - +
219A ASN* 3.9 34.5 - - - +
220A LYS* 3.9 11.4 - - + +
223A ALA* 3.6 4.9 - - + +
310A VAL* 4.0 21.8 - - + -
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Residues in contact with ALA 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 81.1 - - - +
11A LEU* 1.3 63.1 + - - +
12A VAL* 4.2 4.0 - - + -
118A TYR* 3.3 4.5 - - - -
119A VAL* 2.8 43.3 + - + +
121A LEU* 3.7 23.4 - - + +
197A VAL* 3.8 17.3 - - + -
215A GLY 3.1 12.1 - - - +
216A ILE* 4.3 2.0 - - + -
223A ALA* 4.0 3.4 - - - -
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Residues in contact with LEU 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 ALA* 1.3 73.2 - - - +
12A VAL* 1.3 60.8 - - - +
13A ASP* 4.0 9.6 - - + -
116A GLU* 3.9 16.4 - - + +
117A ALA 3.4 27.1 - - - +
118A TYR* 3.5 41.3 - - + -
214A ALA* 3.1 5.2 - - - -
215A GLY 2.9 30.5 + - - -
223A ALA* 3.8 17.2 - - - +
224A LYS* 3.6 27.4 - - + -
227A CYS* 3.8 20.2 - - + -
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Residues in contact with VAL 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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10A ALA* 4.9 1.8 - - + -
11A LEU* 1.3 74.9 - - - +
13A ASP* 1.3 64.2 + - - +
14A MET* 4.2 4.3 - - - -
103A MET* 3.9 22.6 - - + +
115A ASP 3.8 0.3 - - - +
116A GLU* 3.1 25.9 - - - +
117A ALA 3.0 10.9 + - - +
119A VAL* 4.1 13.5 - - + -
197A VAL* 4.6 7.4 - - + -
200A MET* 4.1 23.1 - - - -
201A ARG* 4.9 1.8 - - + -
204A ILE* 4.4 7.2 - - + -
212A CYS* 3.6 31.0 - - + -
213A SER 3.6 3.8 - - - +
214A ALA* 4.1 13.0 - - + -
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Residues in contact with ASP 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 LEU* 4.0 6.5 + - + +
12A VAL* 1.3 76.2 - - - +
14A MET* 1.3 63.8 + - - +
115A ASP* 3.6 2.5 - - - -
116A GLU* 3.2 12.7 - - - +
212A CYS* 3.8 2.9 - - - -
213A SER 3.0 29.4 + - - -
224A LYS* 5.1 3.8 - - - -
227A CYS* 3.7 20.2 - - - -
231A LYS* 3.0 12.4 + - - +
501A MG 2.0 29.6 - - - -
502A CA 2.2 26.5 - - - -
508A STP 2.7 10.3 + - - -
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Residues in contact with MET 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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12A VAL* 4.8 4.9 - - - -
13A ASP* 1.3 71.4 + - - +
15A ASP* 1.3 60.7 + - - +
17A PHE* 3.5 31.0 - - + -
20A GLN* 4.6 0.2 - - - +
99A VAL* 3.7 30.3 - - + -
103A MET* 6.0 0.4 - - - -
115A ASP* 2.9 30.3 + - + +
204A ILE* 3.9 15.5 - - + -
210A PHE* 3.3 35.7 - - + -
211A GLN 3.6 11.9 - - - +
212A CYS* 3.7 16.4 - - + -
502A CA 2.3 32.2 - - - -
508A STP 3.1 0.3 + - - -
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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