Contacts of the helix formed by residues 335 - 349 (chain A) in PDB entry 3Q7I
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.6 5.3 - - + +
153A LYS* 3.2 46.6 + - + +
154A MET* 3.6 28.7 + - + +
157A ARG* 3.9 31.9 - - + -
332A ARG 4.9 1.2 + - - -
333A LEU 3.2 0.6 - - - -
334A CYS* 1.4 92.8 - - - +
336A PHE* 1.3 58.8 + - - +
337A VAL 3.5 1.8 - - - -
338A ASP* 3.3 20.3 + - - +
339A TYR* 3.0 29.1 + - - +
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Residues in contact with PHE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A MET* 3.8 23.1 - - + +
326A LEU* 3.9 19.5 - - + -
328A PRO* 4.3 13.5 - - + -
333A LEU* 3.0 42.7 + - + +
335A TYR* 1.3 73.2 - - - +
337A VAL* 1.3 67.9 + - - +
339A TYR* 3.3 2.3 + - - +
340A LEU* 3.0 54.7 + - + +
395A ILE* 4.5 5.6 - - + -
473A LEU* 4.6 1.3 - - + -
476A LEU* 3.8 34.3 - - + -
477A ILE* 4.1 22.7 - - + -
480A TYR* 4.2 11.2 - + - -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.4 42.2 - - + +
328A PRO* 3.9 19.3 - - + -
333A LEU 4.4 1.0 + - - -
334A CYS 5.1 3.0 + - - +
335A TYR 3.5 0.2 - - - -
336A PHE* 1.3 76.5 - - - +
338A ASP* 1.4 62.5 + - - +
340A LEU* 3.2 1.7 + - - +
341A GLN* 2.8 36.6 + - + +
367A LEU* 4.7 5.2 - - + +
368A TRP* 3.8 11.7 - - - +
369A GLY 3.8 23.3 - - - +
370A GLY* 4.0 9.9 - - - +
371A VAL* 6.4 0.4 - - + -
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.4 25.6 - - + +
153A LYS* 5.4 1.4 + - - -
334A CYS 4.9 3.6 + - - +
335A TYR* 3.3 28.1 + - - +
336A PHE 3.3 0.4 - - - -
337A VAL* 1.4 81.2 - - - +
339A TYR* 1.3 62.1 + - - +
341A GLN* 3.4 18.7 + - - +
342A GLN* 3.2 17.0 + - - +
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.7 14.1 - - + +
151A GLY* 3.3 40.4 - - - -
154A MET* 3.6 26.0 - - + -
261A ARG* 3.2 28.2 + - + -
262A TYR* 4.6 1.4 - - - -
263A SER 5.1 0.5 + - - -
264A LEU* 3.4 20.0 + - + +
335A TYR 3.0 17.1 + - - +
336A PHE* 3.6 4.7 - + - +
337A VAL 3.2 0.2 - - - -
338A ASP* 1.3 77.1 - - - +
340A LEU* 1.3 74.5 + - + +
342A GLN* 3.3 10.3 + - - +
343A ALA* 3.0 26.9 + - + +
477A ILE* 3.9 22.1 - - + +
481A GLU* 4.2 11.0 + - + -
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LEU* 3.8 11.9 - - + -
336A PHE* 3.0 53.5 + - + +
337A VAL 4.1 0.7 - - - +
339A TYR* 1.3 97.1 - - + +
341A GLN* 1.3 60.2 + - - +
343A ALA* 4.2 10.8 - - + +
344A ASP* 2.8 36.5 + - + +
367A LEU* 3.5 15.9 - - + -
477A ILE* 5.0 6.5 - - + +
480A TYR* 3.5 41.7 - - + -
481A GLU* 5.4 1.3 - - + +
484A ILE* 5.2 2.7 - - + -
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A VAL* 2.8 25.6 + - + +
338A ASP* 3.4 19.8 + - - +
339A TYR 3.3 0.2 - - - -
340A LEU* 1.3 71.7 - - - +
342A GLN* 1.3 61.4 + - - +
345A MET* 2.9 46.7 + - - +
366A VAL* 5.4 1.8 - - - +
367A LEU* 2.9 39.8 + - + +
368A TRP* 4.5 7.9 - - - +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLY* 3.6 16.7 - - - +
147A GLY* 3.3 14.9 - - - +
150A LEU* 3.8 20.8 - - + +
261A ARG* 3.9 11.4 - - + +
338A ASP 3.2 9.4 + - - +
339A TYR* 3.5 11.5 - - + +
341A GLN* 1.3 78.8 + - - +
343A ALA* 1.3 66.2 + - - +
346A GLU* 3.0 41.5 + - + +
601A 6PG 3.0 38.6 + - - -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 4.0 25.1 - - - +
262A TYR* 3.7 8.5 + - + -
339A TYR* 3.0 21.2 + - + +
340A LEU* 3.2 15.9 + - + +
342A GLN* 1.3 76.9 - - - +
344A ASP* 1.3 57.5 + - - +
347A SER* 2.5 30.7 + - - -
481A GLU* 5.9 2.9 - - + -
484A ILE* 3.6 19.8 - - + +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A GLN* 4.0 19.1 + - - -
340A LEU* 2.8 22.0 + - + +
341A GLN 4.3 0.4 - - - +
343A ALA* 1.3 72.6 - - - +
345A MET* 1.3 64.6 + - + +
347A SER* 3.1 3.5 + - - -
348A ASN* 2.9 38.8 + - - +
364A GLY* 5.4 3.1 - - - -
365A VAL 4.8 6.3 + - - +
367A LEU* 4.0 23.9 - - + +
483A LYS* 5.1 4.5 + - - +
484A ILE* 3.6 24.4 - - + +
487A GLN* 4.6 8.6 + - - -
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Residues in contact with MET 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLN* 2.9 41.3 + - + +
342A GLN* 5.4 0.2 - - - -
344A ASP* 1.3 72.5 - - + +
346A GLU* 1.3 58.6 + - - +
348A ASN 5.3 0.2 - - - -
349A GLY* 3.0 30.9 + - - +
364A GLY* 6.2 2.2 - - - -
365A VAL 3.7 17.7 - - - +
366A VAL* 3.8 29.4 - - + -
367A LEU* 3.5 25.4 - - + +
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 3.2 24.8 + - - +
341A GLN 4.0 0.2 + - - -
342A GLN* 3.0 32.9 + - + +
345A MET* 1.3 79.6 - - - +
347A SER* 1.3 61.9 + - - +
349A GLY 5.1 0.5 - - - +
350A LYS* 3.6 16.6 + - - -
497A ASP 3.9 1.0 - - - +
498A GLN* 3.3 9.4 - - + +
501A VAL* 3.2 31.0 - - + +
601A 6PG 2.5 42.4 - - - +
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ARG* 2.9 13.5 + - - +
262A TYR* 2.8 17.0 + - - -
343A ALA 2.5 25.0 + - - -
344A ASP 3.1 3.4 + - - -
346A GLU* 1.3 79.3 - - - +
348A ASN* 1.3 67.4 + - - +
349A GLY 3.6 0.2 - - - -
350A LYS* 2.8 26.0 + - - +
484A ILE* 3.6 17.3 - - - -
495A SER* 3.2 24.6 + - - -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A ASP* 2.9 16.7 + - - +
347A SER* 1.3 77.4 - - - +
349A GLY* 1.3 58.8 + - - +
350A LYS* 3.0 9.1 + - - -
363A THR* 3.4 6.1 + - - -
364A GLY* 3.0 31.0 + - - -
484A ILE* 3.1 36.7 + - - +
487A GLN* 3.8 21.8 - - - +
488A GLY* 3.8 1.3 - - - +
491A TRP* 4.0 14.1 - - + -
493A ILE* 3.6 16.8 - - + +
495A SER* 2.7 26.9 + - - -
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A MET* 3.0 20.2 + - - +
346A GLU 4.5 0.7 - - - +
347A SER 3.6 0.6 - - - -
348A ASN* 1.3 72.8 - - - +
350A LYS* 1.3 70.3 + - - +
363A THR* 4.8 1.3 - - - -
364A GLY* 4.6 7.8 - - - -
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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