Contacts of the strand formed by residues 297 - 304 (chain F) in PDB entry 3QS7
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 TYR 297 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285F TRP* 5.1 9.6 - - + -
292F LEU* 5.0 7.6 - - + -
293F GLU 3.9 7.8 + - - +
294F GLU* 3.9 13.3 + - - +
295F GLY 3.8 0.6 - - - -
296F ASN* 1.4 80.1 + - - +
298F PHE* 1.4 63.2 + - - +
313F LEU* 5.5 7.0 - - + -
314F PHE* 3.5 9.0 - - - +
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Residues in contact with PHE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F TYR* 1.4 75.9 - - - +
299F GLU* 1.3 59.4 + - - +
300F MET* 6.2 0.4 - - + -
312F ILE 3.5 1.7 - - - +
313F LEU* 3.5 5.3 - - - +
314F PHE* 3.0 66.3 + - + -
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Residues in contact with GLU 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 4.3 4.3 + - - -
298F PHE* 1.3 73.4 - - - +
300F MET* 1.3 65.4 + - - +
312F ILE 3.4 4.7 - - - +
313F LEU* 3.8 24.2 - - + -
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Residues in contact with MET 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 3.5 11.0 - - - +
180F ASP* 3.5 47.1 - - + +
222F HIS 5.0 2.2 - - - +
224F LEU* 3.6 35.9 - - + -
225F PHE* 3.9 16.2 - - + -
298F PHE* 6.2 0.7 - - + -
299F GLU* 1.3 75.5 - - - +
301F SER* 1.3 63.1 - - - +
311F ARG* 3.7 2.6 - - - +
312F ILE* 2.9 46.7 + - + +
314F PHE* 3.6 31.0 - - + -
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Residues in contact with SER 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B SER* 5.2 7.2 + - - -
11B ILE 3.8 6.9 + - - -
12B SER* 3.3 10.1 - - - -
13B SER* 2.6 47.5 + - - -
14B ASP 3.7 0.5 + - - -
225F PHE* 3.3 5.2 - - - -
300F MET* 1.3 78.8 - - - +
302F THR* 1.4 62.6 + - - +
309F MET* 6.4 0.9 - - - -
310F ILE 3.4 11.7 - - - -
311F ARG* 4.8 5.4 - - - -
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Residues in contact with THR 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 3.7 10.4 + - - -
14B ASP* 3.6 23.6 + - + +
78B GLU* 4.5 3.1 + - - -
225F PHE* 3.4 39.9 - - + -
301F SER* 1.4 74.6 - - - +
303F TYR* 1.3 75.0 + - - +
309F MET* 3.5 5.5 - - - +
310F ILE* 3.0 41.7 + - + +
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Residues in contact with TYR 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 2.6 34.2 + - - +
12B SER* 3.7 15.9 - - - -
77B THR* 3.7 37.5 + - + +
78B GLU* 3.5 37.9 + - - +
81B PHE* 4.7 4.0 - - - +
279F HIS* 4.2 18.1 + - + +
302F THR* 1.3 90.1 + - - +
304F SER* 1.3 61.4 + - - +
307F ARG* 4.3 17.9 - - + -
308F THR 3.2 18.8 - - - -
309F MET* 4.9 8.3 - - + -
310F ILE* 4.0 2.8 - - - +
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Residues in contact with SER 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F VAL* 5.2 2.3 - - - +
303F TYR* 1.3 73.8 - - - +
305F THR* 1.4 86.3 + - - +
307F ARG* 3.4 1.9 + - - -
308F THR* 2.8 46.3 + - - +
310F ILE* 3.5 24.7 - - - -
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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