Contacts of the strand formed by residues 288 - 292 (chain H) in PDB entry 3SRF
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 GLY 288 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266H ILE 3.3 4.8 + - - -
267H ILE* 3.7 17.0 - - - +
268H SER 3.1 19.9 + - - -
283H LEU* 5.3 0.7 - - - -
286H SER* 3.2 12.4 - - - -
287H ASP* 1.3 80.5 - - - +
289H ILE* 1.3 65.3 + - - +
321H LYS* 4.5 5.4 - - - -
322H PRO* 3.3 14.8 - - - -
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Residues in contact with ILE 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267H ILE* 3.8 5.3 - - - +
268H SER* 3.5 25.8 - - - +
270H ILE* 4.2 8.7 - - + -
279H PHE* 3.7 33.2 - - + -
282H ILE* 3.9 17.3 - - + -
283H LEU* 4.0 13.2 - - + -
286H SER* 4.3 3.6 - - - +
288H GLY* 1.3 81.7 - - - +
290H MET* 1.3 73.3 + - - +
291H VAL 4.5 0.7 - - - +
312H MET* 4.6 7.0 - - + -
316H CYS* 3.6 22.4 - - - -
322H PRO 2.9 6.9 + - - +
323H VAL* 3.3 10.8 - - + +
324H ILE* 2.8 26.3 + - - +
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Residues in contact with MET 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ASP* 4.7 1.3 - - - +
240H PHE* 4.4 17.9 - - - -
267H ILE* 3.7 14.1 - - + +
268H SER 3.0 8.1 + - - +
269H LYS* 3.6 39.0 - - + +
270H ILE* 3.1 28.8 + - - +
289H ILE* 1.3 75.3 - - - +
291H VAL* 1.3 62.4 + - - +
292H ALA* 3.2 14.3 + - + -
324H ILE* 3.4 23.1 - - + +
326H ALA* 3.8 17.0 - - + -
359H MET* 4.1 21.1 - - + +
534H PYR 3.7 24.2 - - - +
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Residues in contact with VAL 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H ILE 4.7 0.2 - - - -
289H ILE* 4.7 0.7 - - + -
290H MET* 1.3 70.8 - - - +
292H ALA* 1.3 56.2 + - - +
293H ARG* 3.0 28.1 + - + +
296H LEU* 4.7 5.6 - - + -
305H VAL 5.6 0.7 - - - +
309H GLN* 3.9 26.9 - - + +
312H MET* 3.8 47.6 - - + -
313H ILE* 4.8 3.8 - - + -
323H VAL* 4.2 15.5 - - + -
324H ILE 2.7 17.6 + - - +
325H CYS* 4.6 6.1 - - - -
326H ALA* 3.4 21.8 + - - +
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Residues in contact with ALA 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269H LYS* 4.5 2.2 - - + -
270H ILE 3.3 18.5 + - - +
271H GLU* 3.5 21.7 - - + +
290H MET* 3.2 30.2 + - + +
291H VAL* 1.3 67.2 - - - +
293H ARG* 1.3 63.9 + - - +
294H GLY 3.3 3.0 + - - -
295H ASP 3.7 0.2 + - - -
296H LEU* 3.2 24.4 + - - +
327H THR* 4.5 1.8 - - - -
534H PYR 3.4 18.7 - - - +
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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