Contacts of the strand formed by residues 258 - 262 (chain E) in PDB entry 1QRP
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 258 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197E ILE* 3.5 28.7 - - + -
198E THR 3.5 5.4 - - - +
199E MET* 4.2 14.8 - - + -
204E ILE* 4.1 13.5 - - + -
231E ILE* 4.3 2.2 - - + -
235E ILE* 4.0 13.2 - - + -
256E PRO 3.7 0.6 + - - -
257E ASP* 1.3 74.6 - - - +
259E VAL* 1.3 61.3 + - - +
260E PHE* 4.0 14.5 + - + -
267E TYR 4.0 0.7 - - - +
268E PRO* 3.6 0.2 - - - +
269E VAL* 2.7 42.3 + - + +
274E TYR* 3.7 34.1 - - + +
286E PHE* 3.7 29.6 - - + -
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Residues in contact with VAL 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196E SER 3.7 1.0 - - - +
197E ILE* 3.3 6.9 - - - +
198E THR* 2.8 55.9 + - - +
199E MET* 5.9 0.4 - - - -
257E ASP* 4.4 11.7 - - + +
258E ILE* 1.3 76.9 - - - +
260E PHE* 1.3 64.0 + - - +
261E THR* 3.8 7.2 + - - +
266E GLN* 3.6 45.5 - - + +
267E TYR 3.8 8.5 - - - +
268E PRO* 4.2 15.7 - - + -
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Residues in contact with PHE 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E VAL* 4.2 9.0 - - + -
196E SER 3.7 3.1 - - - -
197E ILE* 3.6 37.7 - - + -
221E LEU* 4.0 29.6 - - + -
258E ILE* 4.1 16.2 - - + -
259E VAL* 1.3 74.0 - - - +
261E THR* 1.3 58.8 - - - +
262E ILE* 4.4 9.9 - - + -
267E TYR* 2.8 46.0 + - + +
269E VAL* 3.9 30.5 - - + -
286E PHE* 4.3 12.3 - + - -
299E TRP* 5.0 5.8 - + - -
301E LEU* 3.8 23.6 - - + -
305E PHE* 4.2 18.4 - + + -
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Residues in contact with THR 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E VAL* 3.7 2.6 - - - +
195E ASP* 2.8 45.1 + - + +
196E SER* 3.0 29.5 + - - +
198E THR* 5.0 2.1 + - - +
259E VAL* 3.8 6.5 + - - +
260E PHE* 1.3 72.1 - - - +
262E ILE* 1.3 64.6 + - - +
264E GLY* 4.0 15.7 - - - +
265E VAL 3.3 11.9 - - - +
266E GLN* 3.9 18.4 - - + +
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Residues in contact with ILE 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E VAL* 3.7 33.3 - - + +
192E ILE* 4.0 16.4 - - + -
193E THR 3.6 16.4 - - - +
194E VAL* 4.1 14.6 - - + -
195E ASP* 4.2 0.2 - - - -
260E PHE* 4.4 9.2 - - + +
261E THR* 1.3 79.0 - - - +
263E ASN* 1.3 64.8 + - - +
265E VAL* 2.8 32.4 + - - +
267E TYR* 3.7 26.4 + - + -
301E LEU* 4.3 9.0 - - + -
305E PHE* 3.9 22.7 - - + -
322E LEU* 4.2 7.9 - - + -
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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