Contacts of the strand formed by residues 312 - 317 (chain R) in PDB entry 5A31
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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272R ALA* 4.2 4.3 - - - +
273R CYS* 3.6 19.6 - - - -
284R GLY* 4.1 6.4 - - - +
285R SER 3.1 20.2 + - - +
288R HIS 3.7 25.4 - - - +
289R ARG 4.2 0.9 - - - +
290R ILE* 3.8 30.7 - - + -
308R HIS* 3.6 29.6 - - + -
311R GLU* 1.3 79.9 - - - +
313R CYS* 1.3 59.6 + - - +
314R GLY 3.9 18.2 - - - +
315R LEU* 4.1 1.8 - - + -
326R SER* 4.6 0.9 - - - -
327R GLY 4.0 6.1 - - - +
328R GLY* 4.2 1.6 - - - -
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Residues in contact with CYS 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189R TYR* 4.2 38.5 - - + +
272R ALA* 4.8 3.8 - - + +
273R CYS* 3.9 14.9 - - - +
311R GLU* 4.2 6.5 - - + +
312R VAL* 1.3 75.2 - - - +
314R GLY* 1.3 58.0 + - - +
327R GLY 3.0 14.3 + - - -
328R GLY 3.8 20.0 - - - -
329R ASN* 3.9 6.1 - - - -
353R ALA* 4.5 5.6 - - - -
354R VAL 3.8 10.8 - - - -
355R LYS* 3.4 31.6 - - + +
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Residues in contact with GLY 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273R CYS* 4.1 2.7 - - - -
312R VAL* 3.8 2.5 - - - +
313R CYS* 1.3 75.9 - - - +
315R LEU* 1.3 66.8 + - - +
326R SER* 3.3 5.6 - - - -
327R GLY* 2.8 42.1 + - - +
354R VAL 4.0 2.0 + - - -
355R LYS 3.6 19.1 - - - -
357R MET* 4.3 5.4 - - - -
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Residues in contact with LEU 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273R CYS* 3.9 20.1 - - + +
274R LEU 3.9 6.6 - - - +
275R SER* 3.6 17.8 - - - -
282R THR* 3.7 22.4 - - + +
283R SER 3.7 8.3 - - - +
284R GLY* 3.5 30.7 - - - +
290R ILE* 3.9 17.0 - - + -
312R VAL* 4.1 2.2 - - + -
314R GLY* 1.3 80.0 - - - +
316R LYS* 1.3 74.0 + - - +
324R LEU* 4.2 15.5 - - + -
325R ALA 3.5 5.8 - - - +
326R SER* 3.5 24.0 - - - -
357R MET* 4.5 2.2 - - - +
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Residues in contact with LYS 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274R LEU 6.1 0.4 - - - -
275R SER* 3.6 4.0 - - - +
315R LEU* 1.3 81.0 - - - +
317R TRP* 1.3 63.2 + - - +
324R LEU* 3.8 4.4 - - - +
325R ALA* 2.9 34.7 + - + +
357R MET* 3.1 47.8 + - + +
358R ALA* 4.9 5.4 - - - +
359R TRP* 3.1 24.4 + - + +
400R ASN* 5.1 5.1 + - - -
401R MET 4.1 14.5 + - - -
402R VAL* 5.6 3.2 - - - +
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Residues in contact with TRP 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275R SER* 3.0 41.2 + - - +
276R TRP 3.4 24.5 - - - +
277R ASN* 3.1 37.5 - - + +
280R VAL* 4.5 7.3 - - + +
282R THR* 2.9 21.9 + - - -
292R HIS* 3.5 25.4 - + - -
316R LYS* 1.3 78.1 - - - +
318R ASN* 1.3 62.4 + - - +
319R VAL* 4.2 8.4 - - + +
322R ASN* 4.0 8.5 - - - -
323R LYS 3.3 34.8 - - - -
324R LEU* 3.8 15.1 - - + +
338R GLY* 3.4 31.4 - - - -
339R THR* 4.3 2.9 - - - -
359R TRP* 3.7 9.5 - - - +
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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