Contacts of the strand formed by residues 369 - 376 (chain B) in PDB entry 3Q02
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 369 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 3.3 19.6 - - + +
13B SER* 3.5 10.3 - - - +
37B TYR* 3.9 30.7 - - + -
78B LEU* 3.5 8.6 - - + +
82B LEU* 3.9 26.7 - - + -
363B ARG* 3.3 4.7 - - - -
364B HIS* 2.9 28.4 + - - +
367B THR* 2.8 21.9 + - - -
368B GLY* 1.3 76.8 - - - +
370B VAL* 1.3 63.5 + - - +
371B LEU* 3.4 6.0 + - + +
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 2.9 29.7 + - - +
17B VAL* 4.4 5.4 - - + -
36B PRO* 3.6 14.8 - - + +
37B TYR* 3.3 23.0 + - - +
256B ALA* 4.8 7.0 - - - +
259B ILE* 4.1 26.7 - - + -
361B VAL* 4.0 9.0 - - + -
362B VAL 3.8 2.9 - - - -
363B ARG* 4.7 2.5 - - + +
368B GLY 4.2 6.3 - - - +
369B THR* 1.3 72.4 - - - +
371B LEU* 1.3 58.8 + - - +
372B PHE 3.7 12.1 - - - +
373B MET* 3.3 28.0 - - + -
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 2.7 31.2 + - - -
36B PRO* 4.3 0.9 - - - -
37B TYR* 3.9 28.0 - - + -
82B LEU* 4.1 22.4 - - + -
83B MET* 5.8 1.6 - - - -
91B ILE* 4.3 23.3 - - + -
169B LEU* 4.8 2.6 - - + +
233B LEU* 3.6 31.2 - - + -
362B VAL* 2.8 19.6 + - + +
364B HIS* 4.1 13.9 - - + +
369B THR* 3.4 8.5 + - + +
370B VAL* 1.3 72.3 - - - +
372B PHE* 1.3 78.2 + - + +
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Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.9 2.0 - - + -
34B PHE 3.2 11.4 - - - +
35B SER* 4.0 2.2 - - - -
36B PRO* 4.1 2.5 - - - -
91B ILE* 4.6 14.8 - - + -
169B LEU* 3.7 43.3 - - + -
171B PHE* 3.5 39.3 - + + -
324B VAL* 3.8 23.3 - - + -
326B ILE* 4.8 6.1 - - + -
360B PHE* 4.7 8.5 - - + -
361B VAL* 3.4 6.4 - - - +
362B VAL* 2.9 57.8 + - + +
370B VAL* 3.7 2.1 - - - +
371B LEU* 1.3 94.0 - - + +
373B MET* 1.3 64.9 + - - +
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Residues in contact with MET 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 3.4 32.5 - - + -
20B PHE* 3.6 40.6 - - + -
33B VAL* 3.7 1.0 - - - +
34B PHE* 2.8 32.3 + - - +
36B PRO* 3.9 13.2 - - + -
254B LEU* 4.7 9.9 - - + -
259B ILE* 3.7 18.6 - - + -
359B LEU* 5.5 1.6 - - + -
360B PHE* 3.5 18.7 - - - +
361B VAL* 3.9 9.6 - - + -
370B VAL* 3.3 27.6 - - + -
372B PHE* 1.3 75.6 - - - +
374B GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.0 7.6 - - - -
32B VAL 2.9 14.4 - - - -
359B LEU* 3.1 21.9 - - - +
360B PHE* 3.1 37.3 + - - -
373B MET* 1.3 79.0 - - - +
375B GLN* 1.3 59.8 + - - -
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Residues in contact with GLN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 4.4 2.6 - - + -
24B ALA* 3.6 26.6 + - - +
27B SER 3.1 20.4 + - - -
28B LYS 3.9 11.2 + - - +
30B ARG 2.8 26.5 + - - +
31B ASN* 3.5 6.8 - - - +
32B VAL* 2.8 38.2 + - + +
247B LEU* 4.3 4.3 - - + +
251B THR* 4.3 10.4 + - - -
280B LEU* 4.1 2.1 - - - +
358B PHE 3.4 9.2 - - - +
359B LEU* 4.1 9.2 - - + -
360B PHE* 3.9 0.4 - - - -
374B GLY* 1.3 74.4 - - - +
376B VAL* 1.3 63.7 + - - +
377B MET* 4.1 16.6 - - - +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 3.7 6.1 - - - +
189B PHE* 4.0 1.0 - - - -
278B PHE* 4.0 22.7 - - + -
280B LEU* 4.3 3.6 - - + -
357B PRO* 3.1 25.5 - - - +
358B PHE* 3.0 49.3 + - + +
360B PHE* 4.0 15.9 - - + -
375B GLN* 1.3 74.3 - - - +
377B MET* 1.3 61.9 + - - +
378B GLU 4.2 1.8 - - - +
379B PRO* 3.8 39.9 - - + -
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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