Contacts of the strand formed by residues 302 - 307 (chain T) in PDB entry 5Z58
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 302 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151R LEU* 6.3 3.1 - - + -
295T ASP 4.1 0.2 - - - +
296T LEU* 3.8 3.4 - - - +
297T HIS* 3.0 51.3 + - + +
300T ILE* 3.8 18.2 - - + -
301T ASP* 1.3 81.1 - - - +
303T LEU* 1.3 60.7 + - - +
304T VAL* 4.2 5.5 + - + +
314T ILE* 3.3 30.5 - - + -
315T TRP 2.8 24.9 - - - +
316T ASP* 4.3 4.3 - - - +
317T VAL* 4.1 3.5 - - - +
323T VAL* 4.5 5.4 - - + -
359T LEU* 4.8 10.1 - - + -
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Residues in contact with LEU 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253T ILE* 5.6 0.2 - - + -
262T PHE* 3.7 27.1 - - + -
270T VAL* 3.8 22.4 - - + -
284T TYR* 4.4 13.5 - - + -
294T LEU* 4.1 21.5 - - + -
295T ASP 3.5 21.1 - - - +
296T LEU* 3.6 22.9 - - + -
302T VAL* 1.3 74.3 - - - +
304T VAL* 1.3 60.5 + - - +
305T THR* 4.1 9.0 - - + -
314T ILE* 3.5 1.4 - - - -
315T TRP* 2.8 51.1 + - + +
317T VAL* 3.9 9.1 - - + +
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Residues in contact with VAL 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294T LEU* 3.0 3.6 - - - +
295T ASP* 2.8 41.8 + - + +
302T VAL* 4.7 5.6 - - + +
303T LEU* 1.3 78.7 - - - +
305T THR* 1.3 67.8 - - - +
312T ALA* 5.0 3.6 - - + -
313T ARG 3.1 12.6 - - - +
314T ILE* 4.4 9.2 - - + -
326T LEU* 5.3 0.7 - - + -
336T VAL* 3.6 30.3 - - + +
338T CYS* 4.1 20.9 - - + -
345T ILE* 4.1 31.6 - - + -
359T LEU* 5.6 0.4 - - + -
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Residues in contact with THR 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270T VAL* 4.1 17.3 - - + -
287T HIS* 2.6 29.9 + - - -
291T VAL* 4.1 5.4 - - + -
293T GLY 3.2 8.5 - - - -
294T LEU* 3.7 16.6 - - + -
303T LEU* 4.1 9.9 - - + -
304T VAL* 1.3 80.5 - - - +
306T CYS* 1.3 64.2 + - - +
312T ALA* 2.9 9.5 - - - +
313T ARG* 2.9 29.6 + - - +
315T TRP* 2.9 27.6 + - + +
336T VAL* 4.5 0.4 - - - -
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Residues in contact with CYS 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287T HIS* 4.4 0.4 - - - -
291T VAL* 3.2 9.3 - - - +
292T TYR 2.8 23.3 + - - -
293T GLY* 2.8 17.9 + - - +
305T THR* 1.3 75.0 - - - +
307T SER* 1.3 60.8 + - - +
311T THR 3.9 4.0 - - - -
312T ALA* 4.3 2.0 - - - -
333T VAL* 3.3 38.8 - - + +
334T ALA 4.2 2.0 - - - +
335T THR 3.8 2.9 - - - -
336T VAL* 2.9 52.3 - - - -
347T THR* 4.1 0.9 - - - -
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Residues in contact with SER 307 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287T HIS* 3.4 23.1 - - - -
289T SER 3.5 10.4 + - - -
290T ALA 2.7 15.8 + - - -
291T VAL* 4.1 1.3 - - - +
292T TYR 4.1 1.1 - - - +
306T CYS* 1.3 75.6 - - - +
308T ARG* 1.3 75.5 + - - +
309T ASP* 3.0 27.9 + - - +
310T SER* 3.0 12.6 + - - -
311T THR 3.0 8.6 + - - +
333T VAL* 3.2 20.4 + - - +
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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