Contacts of the strand formed by residues 313 - 318 (chain B) in PDB entry 2W8I
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 ALA 313 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A VAL* 3.7 30.3 - - + -
49B LEU 3.9 1.0 + - - -
50B VAL* 3.4 15.1 - - + +
51B ASN* 3.1 23.8 + - - -
301B VAL* 4.6 5.4 - - + -
302B ARG 3.8 11.2 - - - +
303B GLN* 4.5 0.4 - - - -
304B LEU* 4.1 4.1 - - - +
311B LYS* 3.7 1.3 - - - +
312B ILE* 1.3 89.1 - - + +
314B ASP* 1.3 68.5 + - - +
315B ILE* 5.3 1.6 - - + -
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Residues in contact with ASP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN* 3.4 30.4 + - - +
53B TYR* 3.9 15.7 + - + -
300B VAL 3.5 1.0 - - - +
302B ARG* 3.1 37.4 + - + +
304B LEU* 3.6 29.2 - - - +
313B ALA* 1.3 76.9 - - - +
315B ILE* 1.3 64.4 + - - +
316B TYR* 3.5 33.1 + - + +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A SER* 4.0 26.7 - - - -
50B VAL* 4.6 16.6 - - + -
51B ASN 2.7 16.2 + - - +
52B VAL* 3.3 15.0 - - + -
53B TYR* 2.7 34.7 + - - -
299B PHE* 3.9 33.2 - - + -
300B VAL 3.4 8.5 - - - +
301B VAL* 4.5 18.8 - - + -
313B ALA* 4.8 5.8 - - + +
314B ASP* 1.3 80.8 - - - +
316B TYR* 1.3 61.5 - - - +
317B GLN 4.1 0.7 - - - +
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Residues in contact with TYR 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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53B TYR* 3.2 27.0 - + + +
55B MET* 3.6 24.6 - - + +
59B LEU* 3.6 28.3 - - + -
63B LEU* 4.1 22.5 - - + +
298B ILE 3.4 1.7 - - - +
299B PHE* 3.3 4.3 - - - -
300B VAL* 3.1 37.8 + - + +
302B ARG* 4.2 30.1 + - + -
314B ASP* 3.5 40.8 + - + +
315B ILE* 1.3 77.5 - - - +
317B GLN* 1.3 61.1 + - - +
318B LEU 3.9 0.2 + - - -
332B PHE* 4.1 19.3 - + - -
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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
----------------------------------------------------------
52B VAL* 4.7 13.9 - - + +
53B TYR 2.9 10.7 + - - +
54B PRO* 3.7 5.6 - - + +
55B MET* 2.8 25.6 + - - +
296B THR* 3.2 20.6 + - - -
298B ILE 3.4 3.8 - - - -
299B PHE* 3.5 34.7 - - + -
315B ILE 4.1 1.6 + - - -
316B TYR* 1.3 72.3 - - - +
318B LEU* 1.3 71.4 + - - +
319B ASN* 5.1 6.7 - - - +
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Residues in contact with LEU 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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55B MET* 3.7 41.5 - - + +
278B LEU* 4.5 6.7 - - + -
296B THR 3.5 10.2 - - - +
298B ILE* 2.7 46.2 + - + +
317B GLN* 1.3 77.8 - - - +
319B ASN* 1.3 64.6 + - - +
320B ALA* 3.6 17.4 + - + +
325B ALA* 3.9 26.7 - - + +
326B MET* 3.7 31.2 - - + -
328B LEU* 4.2 9.9 - - + -
329B GLY 4.9 1.8 - - - +
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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