Contacts of the helix formed by residues 329 - 339 (chain A) in PDB entry 3JPW
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 ILE 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.2 24.7 - - + -
326A GLU 4.5 2.5 - - - +
327A LYS* 3.0 30.0 + - + +
328A ARG* 1.3 75.5 - - - +
330A TYR* 1.3 68.5 + - - +
332A SER* 3.4 2.5 + - - +
333A ASN* 3.1 40.7 + - - +
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Residues in contact with TYR 330 (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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311A HIS* 5.8 0.9 + - - -
313A PHE* 6.0 1.6 - + - -
327A LYS 5.2 0.2 + - - -
328A ARG 3.4 1.0 + - - -
329A ILE* 1.3 82.2 - - - +
331A GLN* 1.3 70.1 + - + +
333A ASN* 3.5 10.5 + - + +
334A MET* 3.6 34.2 + - + +
611A CL 4.7 19.3 - - + -
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Residues in contact with GLN 331 (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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307A MET* 4.4 2.5 - - - +
313A PHE* 3.2 39.1 - - + -
314A ILE 5.4 0.2 + - - -
315A PRO* 3.4 29.9 - - + +
316A GLU* 3.8 8.7 + - - +
318A LYS* 5.2 3.1 + - - +
328A ARG* 3.4 18.2 + - + +
329A ILE 3.4 0.4 - - - -
330A TYR* 1.3 78.3 - - + +
332A SER* 1.3 70.4 + - - +
334A MET* 2.7 28.5 + - - +
335A LEU* 3.4 2.3 + - - +
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.8 46.5 - - - +
140A SER 5.4 0.9 + - - -
142A MET* 4.0 14.1 - - - +
315A PRO* 4.9 6.7 - - - +
318A LYS* 5.4 3.2 - - - +
328A ARG 3.5 7.2 + - - -
329A ILE 3.4 5.1 + - - -
331A GLN* 1.3 75.5 - - - +
333A ASN* 1.3 84.1 + - - -
334A MET 2.5 13.9 + - - -
335A LEU* 2.7 20.4 + - - +
336A ASN 3.2 7.3 + - - -
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Residues in contact with ASN 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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120A LEU* 5.4 2.2 - - - +
140A SER* 5.7 4.4 + - - +
142A MET* 5.3 0.2 - - - -
329A ILE* 3.1 29.7 + - - +
330A TYR* 3.7 10.3 - - + +
331A GLN 3.2 0.4 + - - -
332A SER* 1.3 91.6 + - - +
334A MET* 1.3 61.4 + - - +
336A ASN* 3.4 20.3 - - - +
337A ARG* 3.7 5.5 + - - +
611A CL 3.8 25.8 - - + +
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Residues in contact with MET 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 3.6 19.5 - - + -
311A HIS* 3.4 42.0 - - + +
313A PHE* 3.2 36.6 - - + -
330A TYR* 3.6 38.7 + - + +
331A GLN* 2.7 18.6 + - - +
332A SER 2.5 5.1 + - - -
333A ASN* 1.3 71.0 - - - +
335A LEU* 1.3 63.8 + - - +
337A ARG* 3.0 21.3 + - - +
338A TYR* 3.6 11.4 - - + -
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Residues in contact with LEU 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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95A GLN 5.0 4.0 - - - +
120A LEU 5.7 0.9 - - - +
122A PRO* 3.7 34.1 - - + -
142A MET* 4.6 5.4 - - + -
300A ILE* 5.4 2.5 - - + +
303A ALA* 3.7 39.7 - - + +
304A ALA* 4.1 7.6 - - + +
307A MET* 3.8 13.2 - - - -
315A PRO* 4.0 28.9 - - + -
331A GLN 3.4 1.2 + - - -
332A SER* 2.7 15.5 + - - +
334A MET* 1.3 74.2 - - - +
336A ASN* 1.3 53.8 + - - +
338A TYR* 2.6 31.8 + - + +
339A LEU* 3.2 14.9 + - + -
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Residues in contact with ASN 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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141A SER 4.3 4.9 - - - +
142A MET* 3.0 34.4 - - + +
144A PHE* 3.7 16.1 - - - -
332A SER 3.2 2.2 + - - -
333A ASN* 3.4 16.2 - - - +
334A MET 3.1 0.6 - - - -
335A LEU* 1.3 79.2 - - - +
337A ARG* 1.3 60.9 + - - +
338A TYR 3.1 0.6 + - - -
339A LEU* 4.2 4.9 - - - -
340A ILE* 3.3 33.4 + - - +
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Residues in contact with ARG 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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333A ASN 3.7 4.9 + - - +
334A MET* 3.0 14.7 + - - +
335A LEU 2.9 0.6 + - - -
336A ASN* 1.3 80.6 - - - +
338A TYR* 1.3 71.7 + - + +
340A ILE* 3.7 17.4 - - - +
341A ASN* 4.1 8.3 + - - +
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Residues in contact with TYR 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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303A ALA* 3.8 24.6 - - + -
306A ASP* 4.0 22.7 - - + +
307A MET* 3.3 42.0 - - + -
310A GLU* 3.2 34.4 + - - +
311A HIS* 3.2 21.2 + + - -
334A MET* 3.6 23.6 - - + -
335A LEU* 2.6 15.0 + - - +
337A ARG* 1.3 77.2 - - + +
339A LEU* 1.3 61.5 + - - +
340A ILE 2.9 5.5 + - - -
341A ASN* 3.1 13.4 + - - +
342A VAL* 3.5 13.5 + - - +
502A NAG 6.3 1.6 - - + -
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Residues in contact with LEU 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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122A PRO* 3.6 39.7 - - + -
124A LEU* 5.8 1.6 - - + -
142A MET* 3.9 20.6 - - + -
144A PHE* 3.7 22.0 - - + -
299A ILE* 3.8 24.2 - - + +
300A ILE* 4.1 14.1 - - + -
303A ALA* 3.4 23.2 - - + +
335A LEU* 3.2 13.2 + - + +
336A ASN* 4.3 2.9 - - - +
338A TYR* 1.3 77.2 - - - +
340A ILE* 1.3 69.6 + - + +
341A ASN 3.3 0.9 + - - -
342A VAL* 3.9 8.3 + - - +
349A LEU 5.0 0.2 - - - +
351A PHE* 3.6 16.9 - - + -
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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