Contacts of the strand formed by residues 308 - 317 (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 THR 308 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275F VAL* 3.9 18.6 - - + -
276F HIS 3.3 23.1 - - - +
277F VAL* 3.5 11.9 - - + -
303F TYR* 3.2 11.4 - - - -
304F SER* 2.8 38.3 + - - +
305F THR* 2.7 26.7 + - - +
306F ASN 3.2 7.7 + - - +
307F ARG* 1.3 74.4 - - - +
309F MET* 1.4 58.3 + - - +
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Residues in contact with MET 309 (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* 3.6 1.8 - - - +
276F HIS 2.9 34.0 + - - -
277F VAL 4.1 0.6 + - - -
278F ASN 4.0 5.2 - - - +
279F HIS* 3.8 33.7 - - + +
281F PHE* 3.6 10.5 - - + -
301F SER* 6.4 0.9 - - - -
302F THR 3.5 7.9 - - - +
303F TYR* 4.9 8.7 - - + -
307F ARG 5.4 0.2 - - - +
308F THR* 1.4 73.5 - - - +
310F ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F PHE* 3.5 24.2 - - + -
226F GLY* 5.4 5.6 - - - +
273F LYS* 5.1 7.4 - - + -
274F ALA 3.6 11.9 - - - +
275F VAL* 3.9 24.7 - - + -
281F PHE* 4.6 0.7 - - - -
301F SER* 3.4 6.8 - - - -
302F THR* 3.0 54.8 + - + +
303F TYR 4.0 2.5 - - - +
304F SER* 3.5 31.2 - - - -
309F MET* 1.3 77.6 - - - +
311F ARG* 1.3 65.0 + - - +
312F ILE* 5.4 0.4 - - + -
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Residues in contact with ARG 311 (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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272F CYS 3.4 1.2 - - - +
273F LYS* 3.3 6.4 - - - +
274F ALA 3.0 31.4 + - - -
281F PHE* 3.8 23.6 - - + +
283F LEU* 3.8 20.4 - - + +
300F MET 3.7 6.7 - - - +
301F SER* 5.1 4.7 - - - -
310F ILE* 1.3 74.7 - - - +
312F ILE* 1.3 63.2 + - - +
313F LEU* 4.1 0.9 - - + -
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Residues in contact with ILE 312 (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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224F LEU* 3.4 31.6 - - + +
225F PHE* 3.5 39.7 - - + -
226F GLY 4.8 1.1 - - - +
271F ARG* 4.4 15.9 - - + -
272F CYS 3.4 4.7 - - - +
273F LYS* 5.0 9.2 - - + -
298F PHE 3.5 1.7 - - - +
299F GLU* 3.4 3.8 - - - +
300F MET* 2.9 54.1 + - + +
310F ILE* 5.4 0.7 - - + -
311F ARG* 1.3 74.9 - - - +
313F LEU* 1.3 61.2 + - - +
314F PHE* 3.6 28.0 - - + +
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Residues in contact with LEU 313 (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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272F CYS* 2.9 19.9 + - + +
283F LEU* 3.4 57.7 - - + +
284F THR* 3.9 9.4 - - - +
285F TRP* 2.5 57.6 + - + +
297F TYR* 5.5 5.8 - - + -
298F PHE 3.5 8.7 - - - +
299F GLU* 3.8 23.3 - - + -
311F ARG* 4.1 0.6 - - + -
312F ILE* 1.3 69.5 - - - +
314F PHE* 1.3 55.6 + - - +
330F CYS* 5.4 0.4 - - - -
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Residues in contact with PHE 314 (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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175F LYS* 4.8 12.1 - - + -
180F ASP* 6.2 2.0 - - - -
181F ALA 6.0 5.2 - - - -
182F LEU* 5.2 2.9 - - + -
224F LEU* 4.5 11.9 - - + -
244F LEU* 6.2 0.4 - - + -
269F TRP* 3.5 38.1 - + + -
270F ILE 3.2 13.5 - - - +
271F ARG* 3.6 16.8 - - + +
285F TRP* 3.5 2.6 + - - -
297F TYR* 3.5 3.9 - - - -
298F PHE* 3.0 64.0 + - + -
300F MET* 3.6 31.0 - - + -
312F ILE* 3.6 17.3 - - + -
313F LEU* 1.3 75.7 - - - +
315F ALA* 1.3 60.4 + - - +
316F PHE* 5.1 1.3 - - + -
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Residues in contact with ALA 315 (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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269F TRP* 3.6 3.3 - - - -
270F ILE* 2.9 49.5 + - + +
285F TRP* 3.3 32.3 - - + +
292F LEU* 4.1 12.1 - - + -
296F ASN 3.2 12.8 - - - +
314F PHE* 1.3 73.4 - - - +
316F PHE* 1.3 62.1 + - - +
328F TYR* 5.7 1.1 - - + -
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Residues in contact with PHE 316 (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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268F LEU* 3.1 12.1 - - - +
269F TRP* 3.5 37.0 - - + -
292F LEU* 5.5 0.2 - - - +
295F GLY 4.4 2.3 - - - +
296F ASN* 3.0 37.4 + - - +
314F PHE* 4.5 1.8 + - + -
315F ALA* 1.3 75.7 - - - +
317F VAL* 1.3 68.1 + - - +
318F SER 4.4 0.2 + - - -
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Residues in contact with VAL 317 (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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267F PRO* 3.1 7.3 - - - +
268F LEU* 2.9 58.4 + - + +
269F TRP* 5.0 0.5 + - - -
296F ASN* 5.5 4.5 - - + -
316F PHE* 1.3 80.9 - - - +
318F SER* 1.3 67.7 + - - +
319F SER 3.5 25.4 - - - +
320F VAL* 3.8 6.3 - - + -
324F ASP* 3.6 29.2 - - + +
328F TYR* 4.6 6.1 - - + +
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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