Contacts of the helix formed by residues 331 - 339 (chain A) in PDB entry 4QNW
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 ASP 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A SER* 3.4 15.3 - - - -
329A THR* 3.8 1.6 - - - +
330A PRO* 1.3 72.9 - - - +
332A LEU* 1.3 64.7 + - - +
333A PRO* 3.3 4.3 - - - -
334A PHE* 3.0 7.6 + - + -
335A ARG* 2.8 51.1 + - - +
364A PHE* 3.7 20.1 - - + -
365A SER* 2.7 39.1 + - - -
368A TYR* 3.3 20.0 - - + +
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Residues in contact with LEU 332 (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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25A MET* 3.9 18.6 - - + -
322A PHE* 3.9 34.1 - - + -
325A TYR* 3.5 41.5 - - + +
326A PHE* 3.8 18.2 - - + +
329A THR* 3.0 25.8 + - + +
330A PRO 3.3 0.8 - - - -
331A ASP* 1.3 76.4 - - - +
333A PRO* 1.3 71.6 - - + +
335A ARG* 3.2 1.8 + - - +
336A VAL* 2.9 37.9 + - + +
342A LEU* 4.0 15.9 - - + -
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Residues in contact with PRO 333 (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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23A HIS* 3.5 42.4 - - + +
25A MET* 3.9 16.2 - - + +
54A SER* 3.7 11.9 - - - +
55A VAL* 4.5 4.0 - - + -
58A THR* 4.1 8.5 - - + +
326A PHE* 3.7 22.7 - - + -
331A ASP 3.4 4.7 - - - -
332A LEU* 1.3 96.6 - - + +
334A PHE* 1.3 61.1 + - - +
336A VAL 4.0 0.2 - - - -
337A MET* 3.0 36.2 + - + +
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Residues in contact with PHE 334 (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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55A VAL* 3.6 25.2 - - + +
331A ASP* 3.0 12.0 + - + +
333A PRO* 1.3 80.2 - - - +
335A ARG* 1.3 63.1 + - - +
337A MET* 3.4 6.6 + - - +
338A ALA* 3.0 30.5 + - + +
340A ILE* 3.5 27.8 - - + -
365A SER* 3.6 10.8 - - - -
367A GLU* 4.2 4.3 - - + -
368A TYR* 3.5 47.8 - + + -
371A LEU* 3.6 32.5 - - + -
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Residues in contact with ARG 335 (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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329A THR* 3.4 19.2 - - - +
331A ASP* 2.8 38.9 + - - +
332A LEU 3.6 5.6 - - - +
334A PHE* 1.3 76.1 - - - +
336A VAL* 1.3 65.6 + - - +
338A ALA 3.1 1.0 + - - -
339A GLY 3.0 4.7 + - - -
340A ILE* 2.8 56.2 + - + +
341A GLN 3.0 27.6 + - - -
342A LEU* 3.9 6.5 - - + -
343A GLN* 3.5 28.7 + - - +
363A PRO* 3.3 27.7 + - - +
364A PHE 3.7 1.2 + - - -
365A SER* 3.4 27.0 - - - +
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Residues in contact with VAL 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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10A LEU* 4.2 9.9 - - + -
11A PHE* 3.7 27.7 - - + -
25A MET* 3.6 24.5 - - - -
300A ALA* 4.0 31.0 - - + +
304A GLU* 5.6 2.0 - - - +
322A PHE* 5.5 2.2 - - + -
332A LEU* 2.9 27.2 + - + +
333A PRO 4.0 0.2 - - - +
335A ARG* 1.3 76.9 - - - +
337A MET* 1.3 61.3 - - - +
338A ALA 3.3 0.3 + - - -
339A GLY* 3.4 10.0 + - - -
340A ILE 4.8 2.2 - - - -
342A LEU* 3.8 21.1 - - + -
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Residues in contact with MET 337 (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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11A PHE* 3.4 55.5 - - + +
22A GLN 5.6 0.4 - - - +
23A HIS* 4.2 17.5 - - + -
25A MET* 3.9 7.9 - - + -
55A VAL* 4.2 22.0 - - + -
333A PRO* 3.0 32.4 + - + +
334A PHE* 4.0 7.0 - - - +
336A VAL* 1.3 76.6 - - - +
338A ALA* 1.3 60.1 + - - +
339A GLY 3.7 0.3 + - - -
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Residues in contact with ALA 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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334A PHE* 3.0 27.3 + - + +
335A ARG 3.1 0.4 + - - -
337A MET* 1.3 80.2 - - - +
339A GLY* 1.3 59.6 + - - +
340A ILE* 3.3 26.0 + - + +
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Residues in contact with GLY 339 (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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335A ARG 3.0 4.4 + - - -
336A VAL* 3.4 10.1 + - - -
337A MET 3.5 1.0 + - - -
338A ALA* 1.3 78.4 - - - +
340A ILE* 1.3 61.4 + - - +
341A GLN 3.9 1.2 + - - -
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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