Contacts of the strand formed by residues 315 - 320 (chain B) in PDB entry 2WQX
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 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ALA* 3.3 16.8 - - + +
244B ASN* 3.7 34.3 - - - +
258B THR* 4.5 7.4 - - - +
259B VAL* 3.5 32.1 - - + -
295B SER* 3.1 8.1 - - - -
296B PHE* 2.8 61.2 + - + -
298B PHE* 4.2 6.3 - - + -
314B ARG* 1.3 77.6 - - - +
316B THR* 1.3 64.7 + - - +
317B GLN* 4.0 0.8 + - + +
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Residues in contact with THR 316 (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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242B ALA 2.8 15.3 + - - -
243B LEU* 3.7 17.7 - - + -
244B ASN* 2.8 33.8 + - - +
293B GLU* 3.3 42.2 + - + +
294B VAL 3.9 2.0 - - - +
295B SER* 4.3 4.2 - - - -
314B ARG* 3.9 20.6 + - - -
315B VAL* 1.3 76.0 - - - +
317B GLN* 1.3 57.9 + - - +
318B PRO* 3.5 5.0 - - + +
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Residues in contact with GLN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN* 2.9 32.1 + - - +
245B LYS 3.0 24.0 + - - +
247B ILE* 3.6 24.6 - - + +
255B VAL* 3.8 22.2 - - + +
285B TRP* 5.2 4.0 - - + -
293B GLU* 3.2 3.5 - - - -
294B VAL* 2.8 45.7 + - + +
295B SER* 5.5 0.2 - - - -
296B PHE* 6.1 2.2 - - + -
315B VAL* 4.0 0.6 + - + +
316B THR* 1.3 70.8 - - - +
318B PRO* 1.3 93.6 + - - +
319B LEU* 3.8 15.5 - - + +
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Residues in contact with PRO 318 (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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243B LEU* 3.5 19.7 - - + -
244B ASN 3.1 23.8 - - - +
246B PRO* 4.3 19.5 - - + -
247B ILE 3.4 9.4 + - - -
292B ASN 3.5 10.1 - - - +
293B GLU* 4.2 4.3 - - + -
316B THR* 3.5 9.6 - - + +
317B GLN* 1.3 104.7 + - - +
319B LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 319 (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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246B PRO* 5.5 1.3 - - - -
247B ILE* 3.3 31.9 - - + +
248B ASN 4.5 1.6 - - - +
249B HIS* 4.2 17.5 - - + -
253B LEU* 3.8 17.9 - - + -
287B LEU* 3.6 31.9 - - + -
290B PHE* 3.5 15.6 - - - -
291B THR* 3.4 29.4 - - + +
292B ASN* 2.9 12.2 + - - +
293B GLU 4.3 2.2 - - - +
294B VAL* 4.3 6.7 - - + -
317B GLN* 3.8 11.7 - - + +
318B PRO* 1.3 85.0 - - - +
320B LYS* 1.3 59.8 + - - +
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Residues in contact with LYS 320 (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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246B PRO* 5.1 9.4 - - + -
247B ILE 2.7 19.5 + - - +
248B ASN* 3.6 23.0 + - - +
249B HIS* 2.8 29.1 + - - +
290B PHE* 3.7 2.9 - - - -
319B LEU* 1.3 73.6 - - - +
321B GLU* 1.3 78.1 + - - +
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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