Contacts of the helix formed by residues 312 - 322 (chain J) in PDB entry 2QJK
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 312 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307J ALA 3.7 11.7 - - - +
308J PHE* 4.0 14.8 - - + -
309J THR* 3.1 30.7 + - - +
310J ALA 3.5 0.6 - - - -
311J ASP* 1.3 80.0 - - - +
313J TRP* 1.3 60.4 + - + +
314J VAL* 3.9 14.4 - - + +
315J VAL* 3.2 29.3 - - + +
316J GLN* 2.6 29.2 - - - +
394J LEU* 3.9 25.1 - - + -
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Residues in contact with TRP 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311J ASP 4.6 7.4 + - - -
312J VAL* 1.3 73.2 - - + +
314J VAL* 1.3 61.3 + - + +
315J VAL 3.0 2.0 - - - -
316J GLN* 2.7 36.3 + - - +
317J ILE* 3.0 13.7 + - + +
313M TRP* 3.5 89.7 - + + +
316M GLN* 4.2 18.8 + - + +
317M ILE* 4.1 22.7 - - + -
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Residues in contact with VAL 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 5.5 4.9 - - + -
312J VAL* 3.7 10.0 - - + +
313J TRP* 1.3 78.3 - - + +
315J VAL* 1.3 61.1 + - - +
317J ILE* 3.4 20.9 - - + +
318J ALA* 3.2 20.8 + - - +
331J PHE* 3.6 23.6 - - + -
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Residues in contact with VAL 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 3.8 10.3 - - + -
309J THR 4.0 8.5 - - - +
310J ALA* 4.9 4.3 - - - +
312J VAL* 3.2 31.4 - - + +
313J TRP 2.9 0.2 + - - -
314J VAL* 1.3 76.2 - - - +
316J GLN* 1.3 54.5 + - + +
318J ALA* 3.0 7.1 - - - +
319J ASN* 2.7 35.6 + - + +
326J ILE 4.3 0.5 - - - +
327J ASP 4.5 3.8 - - - -
328J ALA* 3.9 29.8 - - + +
331J PHE* 3.6 38.4 - - + -
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Residues in contact with GLN 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310J ALA 3.3 24.4 + - - +
311J ASP* 3.4 20.4 + - - +
312J VAL 2.6 25.4 - - - +
313J TRP* 2.7 15.9 + - - +
315J VAL* 1.3 70.3 - - + +
317J ILE* 1.3 68.7 + - - +
319J ASN* 3.3 11.9 + - - +
320J PHE* 3.0 20.3 + - - +
313M TRP* 3.6 26.3 + - + -
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Residues in contact with ILE 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313J TRP* 3.0 13.6 + - + +
314J VAL* 3.4 24.5 - - + +
316J GLN* 1.3 74.7 - - - +
318J ALA* 1.3 55.3 + - + +
320J PHE* 2.8 26.2 + - - +
321J ILE* 2.9 38.7 + - + +
313M TRP* 4.2 23.5 - - + -
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Residues in contact with ALA 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314J VAL 3.5 9.0 - - - +
315J VAL 3.0 13.7 - - - +
317J ILE* 1.3 78.7 - - + +
319J ASN* 1.3 63.1 + - - +
320J PHE 3.0 1.6 - - - -
321J ILE* 4.0 7.1 - - - +
322J SER* 3.1 28.6 + - - -
326J ILE* 3.9 17.5 - - + +
331J PHE* 3.9 22.0 - - + -
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Residues in contact with ASN 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J VAL* 2.7 21.6 + - + +
316J GLN* 3.5 12.5 - - - +
318J ALA* 1.3 73.0 - - - +
320J PHE* 1.3 58.0 + - - +
322J SER* 3.3 4.2 + - - -
324J GLY* 2.9 44.1 + - - +
326J ILE 3.4 17.6 + - - +
327J ASP* 4.5 11.1 - - - +
328J ALA 5.5 0.8 - - - +
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Residues in contact with PHE 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316J GLN 3.0 10.3 + - - +
317J ILE* 2.8 13.3 + - - +
319J ASN* 1.3 74.9 - - - +
321J ILE* 1.3 73.5 + - + +
322J SER 2.9 6.0 + - - -
323J PHE* 2.9 17.7 + - - +
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Residues in contact with ILE 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317J ILE* 2.9 39.0 + - + +
318J ALA* 3.5 6.7 + - - +
320J PHE* 1.3 83.7 - - + +
322J SER* 1.3 57.9 + - - +
323J PHE* 3.8 15.6 - - - -
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Residues in contact with SER 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318J ALA 3.1 16.9 + - - -
319J ASN 3.3 7.1 + - - -
320J PHE 2.9 1.4 + - - -
321J ILE* 1.3 78.8 - - - +
323J PHE* 1.3 76.7 + - - +
325J ILE* 3.4 20.8 + - - +
326J ILE* 2.7 48.6 + - - -
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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