Contacts of the strand formed by residues 312 - 316 (chain B) in PDB entry 5WN0
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 ILE 312 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 3.2 3.3 - - - -
66B SER* 2.8 50.6 + - - +
209B GLY 4.8 0.7 - - - +
265B THR* 3.6 31.2 - - + -
283B ASP* 3.7 14.8 - - + +
284B TYR* 3.4 41.1 - - - +
285B PHE* 3.5 20.3 - - + -
299B LYS 3.4 15.9 - - - +
300B ILE* 4.4 6.5 - - + -
301B ARG 4.8 0.2 - - - +
310B CYS 4.7 0.4 - - - +
311B PRO* 1.3 77.3 - - - +
313B THR* 1.3 63.6 + - - +
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Residues in contact with THR 313 (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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63B LYS* 4.9 7.6 - - - -
64B ILE 3.0 4.3 - - - +
65B CYS* 3.5 29.6 - - + -
87B GLU* 3.3 26.5 - - + +
285B PHE* 3.5 6.5 - - - -
298B SER* 3.6 3.1 - - - -
299B LYS* 2.8 39.6 + - - +
301B ARG* 2.9 33.3 + - + +
312B ILE* 1.3 80.5 - - - +
314B LEU* 1.3 61.3 + - - +
315B TYR* 5.3 2.2 - - - -
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Residues in contact with LEU 314 (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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62B LEU 3.4 1.0 - - - +
63B LYS* 3.2 7.8 - - - +
64B ILE* 2.6 44.4 + - + +
206B VAL* 3.9 15.7 - - + -
252B SER* 3.9 14.4 - - - +
285B PHE* 3.6 47.8 - - + -
287B LEU* 4.0 8.7 - - + -
295B LEU* 4.0 23.8 - - + -
297B ASP 3.8 2.7 - - - +
298B SER* 4.4 1.6 - - - +
313B THR* 1.3 74.1 - - - +
315B TYR* 1.3 62.2 + - - +
316B LEU* 3.7 31.0 - - + -
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Residues in contact with TYR 315 (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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50B ASP* 2.7 38.4 + - + -
51B GLN 4.1 11.4 - - - -
52B LYS* 3.8 27.0 - - + -
60B ALA* 4.1 16.2 - - + -
62B LEU 3.3 5.2 - - - -
63B LYS* 3.0 54.7 + - + -
295B LEU* 3.9 1.0 - - - +
296B CYS* 3.0 39.1 + - + +
297B ASP* 3.0 23.6 + - + +
299B LYS* 4.3 7.6 - - + -
301B ARG* 3.7 5.8 + - - -
313B THR* 5.0 2.7 - - - -
314B LEU* 1.3 75.9 - - - +
316B LEU* 1.3 67.0 + - - +
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Residues in contact with LEU 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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60B ALA* 4.0 3.8 - - - -
61B THR 3.1 19.9 + - - -
62B LEU* 2.9 32.2 + - + +
165B PHE* 5.9 0.9 - - + -
206B VAL* 4.2 20.2 - - + -
287B LEU* 4.1 18.2 - - + -
291B LEU* 4.6 11.0 - - + +
294B ALA* 3.8 7.9 - - + +
295B LEU* 3.7 23.3 - - + +
314B LEU* 3.7 27.3 - - + -
315B TYR* 1.3 80.6 - - - +
317B ALA* 1.3 59.1 + - - +
318B LEU* 3.3 28.5 + - + -
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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