Contacts of the helix formed by residues 367 - 380 (chain B) in PDB entry 3C7N
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 GLU 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 4.2 4.2 + - - -
669A SO4 5.4 0.5 + - - -
10B ASP* 5.9 1.6 - - - -
17B CYS* 3.7 23.5 - - - -
28B ILE* 4.0 19.1 - - + +
36B ARG* 3.0 39.9 + - - +
37B THR* 5.3 0.9 - - + +
363B ILE* 5.0 2.5 - - + -
364B ASN* 3.0 43.3 + - + +
365B PRO 2.8 0.8 + - - -
366B ASP* 1.3 92.9 - - - +
368B ALA* 1.3 65.5 + - - +
369B VAL* 3.3 3.1 - - - +
370B ALA* 3.6 4.1 + - - +
371B TYR* 3.1 22.7 + - + +
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Residues in contact with ALA 368 (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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179B ALA* 4.4 5.7 - - + -
182B ALA* 3.7 6.9 - - + +
183B TYR* 4.5 19.5 - - + -
336B LEU 4.8 0.9 - - - +
337B VAL* 4.4 18.6 - - + -
363B ILE* 4.2 9.0 - - + +
364B ASN 3.0 12.0 + - - +
365B PRO* 3.5 16.1 + - + +
367B GLU* 1.3 76.9 - - - +
369B VAL* 1.3 59.4 + - - +
371B TYR* 2.8 27.6 - - - +
372B GLY* 3.0 6.1 + - - -
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Residues in contact with VAL 369 (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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10B ASP* 3.6 17.3 - - - +
145B THR* 3.9 20.9 - - + +
175B GLU* 3.9 28.7 - - + +
178B ALA* 3.7 25.0 - - + +
179B ALA* 4.4 6.3 - - + +
199B ASP* 4.7 7.9 - - - +
337B VAL* 3.7 26.0 - - + -
365B PRO 5.6 0.4 - - - +
367B GLU* 3.3 1.5 - - - -
368B ALA* 1.3 73.6 - - - +
370B ALA* 1.3 64.9 + - - +
372B GLY* 2.8 14.0 + - - -
373B ALA* 3.0 10.9 + - - +
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Residues in contact with ALA 370 (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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8B GLY 4.2 3.2 - - - +
10B ASP* 3.8 17.0 + - + +
17B CYS* 3.4 48.2 - - + +
18B VAL 4.4 0.9 - - - +
19B GLY* 4.4 3.5 - - - +
28B ILE* 4.3 7.4 - - + -
367B GLU* 3.6 5.0 + - - +
368B ALA 3.5 0.2 - - - -
369B VAL* 1.3 78.2 - - - +
371B TYR* 1.3 61.9 + - - +
373B ALA* 3.4 8.1 + - - +
374B ALA* 3.0 25.3 + - - +
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Residues in contact with TYR 371 (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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21B PHE* 5.5 1.0 - + - -
25B LYS* 3.9 13.5 - - + +
26B VAL* 3.4 58.2 + - + +
28B ILE* 4.3 8.2 - - + +
182B ALA* 3.4 34.5 - - + -
363B ILE* 4.0 25.1 - - + -
367B GLU* 3.1 14.9 + - + +
368B ALA* 2.8 18.6 - - - +
369B VAL 3.0 0.2 - - - -
370B ALA* 1.3 75.2 - - - +
372B GLY* 1.3 59.9 + - - -
374B ALA* 3.0 14.6 + - - +
375B VAL* 3.1 22.8 + - + +
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Residues in contact with GLY 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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173B ILE* 5.2 0.2 - - - -
178B ALA* 3.1 28.7 - - - -
181B ILE* 3.3 18.2 - - - +
182B ALA* 3.7 6.0 - - - +
368B ALA 3.0 4.4 + - - -
369B VAL 2.8 10.2 + - - -
371B TYR* 1.3 74.4 - - - +
373B ALA* 1.3 60.5 + - - -
375B VAL* 3.2 6.9 + - - +
376B GLN* 3.1 18.7 + - - +
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Residues in contact with ALA 373 (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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8B GLY* 3.7 22.6 - - - -
9B ILE 4.1 1.3 - - - +
143B VAL* 3.8 13.7 - - + +
145B THR* 3.7 28.9 - - + -
173B ILE* 4.2 10.8 - - - -
178B ALA* 4.1 2.0 - - - +
369B VAL 3.0 8.6 + - - +
370B ALA* 3.7 9.6 - - - +
372B GLY* 1.3 75.3 - - - +
374B ALA* 1.3 61.8 + - - +
376B GLN* 3.2 3.0 + - - +
377B ALA 3.1 20.1 + - - -
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Residues in contact with ALA 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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6B ALA 4.5 1.7 - - - +
7B VAL 4.7 0.7 - - - -
8B GLY* 3.7 9.4 - - - +
19B GLY 3.3 35.0 - - - +
20B VAL* 3.7 4.5 - - - +
21B PHE* 3.4 19.2 + - - +
26B VAL* 3.5 14.6 - - + -
370B ALA 3.0 15.6 + - - +
371B TYR 3.0 4.7 + - - +
373B ALA* 1.3 73.7 - - - +
375B VAL* 1.3 64.0 + - - +
377B ALA* 3.9 2.4 + - - +
378B ALA 3.5 10.9 + - - -
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Residues in contact with VAL 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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21B PHE* 4.5 14.6 - - + -
26B VAL* 3.6 15.9 - - + -
181B ILE* 3.8 20.2 - - + +
182B ALA* 4.8 2.5 - - - +
187B LYS* 6.0 1.1 - - - +
371B TYR* 3.1 27.4 + - + +
372B GLY 3.3 8.3 - - - +
374B ALA* 1.3 75.8 - - - +
376B GLN* 1.3 67.1 + - - +
378B ALA* 3.0 20.2 - - + +
379B ILE* 3.1 24.4 + - + +
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Residues in contact with GLN 376 (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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143B VAL* 4.2 13.7 - - + -
171B ARG* 4.0 23.7 + - - -
173B ILE* 4.6 11.1 - - + +
181B ILE* 3.7 26.7 - - + +
186B ASP* 5.8 0.2 + - - -
372B GLY 3.1 9.1 + - - +
373B ALA* 3.2 9.8 + - - +
375B VAL* 1.3 75.8 - - - +
377B ALA* 1.3 56.6 + - - +
378B ALA 2.7 15.5 + - - -
379B ILE* 2.8 41.9 + - - +
380B LEU* 2.8 33.4 + - + +
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Residues in contact with ALA 377 (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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6B ALA* 3.1 36.8 - - + +
7B VAL 3.2 29.4 - - - +
142B ALA 4.8 1.6 - - - -
143B VAL* 3.5 20.7 - - + +
170B LEU* 4.3 3.6 - - + +
373B ALA 3.1 7.6 + - - +
374B ALA 4.3 1.6 - - - +
376B GLN* 1.3 75.0 - - - +
378B ALA* 1.3 63.0 - - - +
380B LEU* 3.9 6.3 - - - +
381B SER* 3.3 11.3 + - - -
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Residues in contact with ALA 378 (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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6B ALA* 4.3 1.0 + - - +
21B PHE* 3.7 32.5 - - + -
374B ALA 3.5 7.9 + - - +
375B VAL* 3.0 14.1 + - + +
376B GLN 2.7 2.8 + - - -
377B ALA* 1.3 69.9 - - - +
379B ILE* 1.3 58.9 + - + +
380B LEU 3.0 1.1 - - - -
381B SER* 2.6 29.6 + - - -
383B ASP* 3.2 26.3 + - - +
384B LYS* 4.0 14.8 - - + -
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Residues in contact with ILE 379 (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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181B ILE* 6.1 0.9 - - + -
186B ASP* 5.5 4.3 - - - +
187B LYS* 4.1 23.1 - - - +
375B VAL* 3.3 25.1 - - + +
376B GLN* 2.8 31.7 + - - +
378B ALA* 1.3 77.0 - - + +
380B LEU* 1.3 60.8 + - + +
381B SER 3.3 3.6 + - - -
382B GLY* 3.8 8.4 + - - -
383B ASP* 4.2 16.9 + - - +
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Residues in contact with LEU 380 (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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143B VAL* 4.1 8.3 - - + -
170B LEU* 4.0 27.9 - - + +
171B ARG* 3.7 57.2 - - + +
376B GLN* 2.8 37.7 + - + +
377B ALA* 3.9 1.6 - - - +
378B ALA 2.7 4.4 + - - -
379B ILE* 1.3 77.3 - - + +
381B SER* 1.3 56.1 + - - -
382B GLY 3.7 0.4 - - - -
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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