Contacts of the strand formed by residues 280 - 285 (chain A) in PDB entry 1JK7
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 GLY 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLY* 3.8 0.9 - - - -
267A PHE 3.3 9.6 - - - -
268A SER* 4.0 11.0 - - - -
270A PRO* 3.6 17.9 - - - +
279A ALA* 1.3 74.7 - - - +
281A ALA* 1.3 58.3 + - - +
295A ILE* 3.4 6.9 - - - +
296A LEU* 2.6 44.3 + - - -
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Residues in contact with ALA 281 (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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63A GLY 4.5 2.4 + - - -
75A LEU* 5.0 2.7 - - - -
253A ASP 4.1 1.3 - - - +
254A GLY* 3.3 30.1 - - - +
255A TYR* 3.7 21.3 - - + +
266A LEU* 4.6 5.2 - - + +
267A PHE 2.9 11.5 + - - +
268A SER* 2.7 30.1 + - - +
280A GLY* 1.3 76.8 - - - +
282A MET* 1.3 60.5 + - - +
293A PHE* 5.3 1.1 - - + -
294A GLN 3.3 9.9 - - - +
295A ILE* 4.6 2.9 - - - -
296A LEU* 5.6 0.4 - - - -
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Residues in contact with MET 282 (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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60A LYS* 4.3 12.6 - - + -
61A ILE 3.5 14.6 - - - +
62A CYS* 3.7 21.8 - - - -
75A LEU* 3.8 38.8 - - + +
78A TYR* 4.3 5.8 - - + -
79A GLY* 3.9 9.9 - - - +
87A TYR* 4.0 18.6 - - - -
266A LEU* 4.9 0.7 - - - -
268A SER* 4.7 0.2 - - - -
281A ALA* 1.3 74.9 - - - +
283A MET* 1.3 65.4 + - - +
293A PHE* 3.5 4.8 - - - -
294A GLN* 2.8 71.9 + - + +
296A LEU* 6.2 0.4 - - + -
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Residues in contact with MET 283 (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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59A LEU 3.9 0.3 - - - +
60A LYS* 3.6 0.9 - - - -
61A ILE* 2.8 56.8 + - + +
169A ILE* 4.7 3.8 - - + -
243A LEU* 4.5 12.1 - - + -
245A CYS* 4.0 15.3 - - + -
257A PHE* 6.0 0.4 - - - -
264A VAL* 4.3 12.1 - - - -
266A LEU* 3.9 14.9 - - + +
282A MET* 1.3 74.4 - - - +
284A SER* 1.3 67.9 + - - +
285A VAL* 3.8 14.6 + - + +
291A CYS* 3.7 28.7 - - + -
292A SER 3.4 8.3 - - - +
293A PHE* 3.4 39.5 - - + -
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Residues in contact with SER 284 (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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59A LEU 3.7 4.7 + - - -
60A LYS* 3.3 36.4 + - - +
282A MET 4.0 1.2 + - - -
283A MET* 1.3 73.5 - - - +
285A VAL* 1.3 65.3 + - - +
286A ASP* 4.0 2.5 + - - +
290A MET 3.5 1.7 - - - +
291A CYS* 3.3 6.6 - - - +
292A SER* 2.7 50.3 + - - -
294A GLN* 4.6 7.9 - - - -
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Residues in contact with VAL 285 (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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57A ALA* 3.3 12.9 - - + +
58A PRO* 3.2 3.7 - - - +
59A LEU* 2.8 38.7 + - + +
61A ILE* 4.1 16.2 - - + -
165A VAL* 4.6 5.8 - - + -
169A ILE* 4.2 8.3 - - + -
283A MET* 3.8 28.0 - - + +
284A SER* 1.3 78.2 + - - +
286A ASP* 1.3 74.2 + - - +
289A LEU* 4.2 11.2 - - + -
290A MET 3.6 2.7 - - - -
291A CYS* 3.9 6.1 - - - -
2024A BME 4.1 19.1 - - - -
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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