Contacts of the helix formed by residues 276 - 281 (chain B) in PDB entry 5J2Q
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 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A LYS* 6.5 1.1 - - + -
261B VAL* 3.6 51.6 - - + +
264B LEU* 4.1 20.2 - - + -
265B ASN* 5.4 10.3 - - + +
274B ILE* 5.6 0.2 - - + -
275B LYS* 1.3 74.1 - - - +
277B ARG* 1.3 64.8 + - - +
278B GLN 3.4 0.7 - - - -
279B LEU* 4.1 8.1 - - + -
280B SER* 2.8 32.0 + - - +
302B GLU* 3.3 7.9 - - - -
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B LYS* 5.5 5.4 - - + -
276B VAL* 1.3 78.9 - - - +
278B GLN* 1.3 74.1 + - + +
280B SER* 3.1 17.9 + - - -
281B LYS* 3.4 21.4 + - - +
302B GLU* 2.8 6.8 + - - +
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Residues in contact with GLN 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 6.0 1.8 - - + -
277B ARG* 1.3 85.9 - - + +
279B LEU* 1.3 62.2 + - - +
281B LYS* 3.2 49.2 + - - +
282B LEU* 3.8 5.0 - - - +
296B THR* 5.1 0.5 + - - -
298B GLU* 3.4 47.2 + - + +
299B ALA* 3.8 26.9 - - - +
302B GLU* 3.0 20.1 + - + +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B TRP* 6.4 0.2 - - + -
257B ILE* 3.8 18.7 - - + +
260B LEU* 3.8 25.6 - - + -
261B VAL* 4.1 7.6 - - + -
264B LEU* 3.7 30.1 - - + -
276B VAL* 4.1 11.9 - - + +
277B ARG 3.3 0.4 - - - -
278B GLN* 1.3 73.8 - - - +
280B SER* 1.3 64.3 + - - +
282B LEU* 3.3 21.9 + - + +
283B LEU 4.2 0.9 + - - -
295B LEU* 4.4 24.2 - - + -
299B ALA* 4.3 18.2 - - + +
302B GLU* 2.7 21.6 + - - +
303B LEU* 4.5 14.4 - - + -
306B ASN* 4.5 5.4 - - - +
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A LYS 4.8 9.2 + - - -
541A GLY 4.8 9.0 - - - +
542A ILE* 4.8 12.4 - - - -
261B VAL* 4.3 22.9 - - - -
276B VAL* 2.8 25.5 + - - +
277B ARG* 3.1 12.1 + - - -
279B LEU* 1.3 76.9 - - - +
281B LYS* 1.3 61.2 + - - +
283B LEU* 3.2 23.2 + - - +
284B ARG* 4.0 2.4 + - - -
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B ARG* 3.4 19.5 + - - +
278B GLN* 3.2 51.9 + - - +
280B SER* 1.3 77.0 + - - +
282B LEU* 1.3 67.8 + - + +
283B LEU 3.1 2.2 - - - -
284B ARG* 3.1 54.0 + - - +
298B GLU* 5.5 3.8 + - - +
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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