Contacts of the helix formed by residues 314 - 319 (chain A) in PDB entry 3N6J
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A LEU 3.8 3.8 + - - -
313A ALA* 1.3 70.2 - - - +
315A PRO* 1.3 61.6 - - - +
316A HIS* 2.7 32.1 + - - -
317A PHE* 2.9 34.0 + - + -
318A TRP* 2.7 39.2 + - - +
340A HIS* 2.3 58.6 + - + +
341A SER* 3.9 3.5 + - - -
342A ASN* 4.5 1.2 + - - -
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Residues in contact with PRO 315 (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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115A ALA* 3.3 4.4 - - - +
313A ALA 3.3 6.9 - - - +
314A ASP* 1.3 89.9 - - - +
316A HIS* 1.3 64.2 + - + +
319A THR* 2.6 42.5 + - - +
320A LEU* 4.3 16.8 - - + -
323A ALA* 4.0 1.8 - - + -
339A CYS* 3.8 14.4 - - - -
340A HIS 4.8 0.2 - - - +
351A MSE 5.3 4.0 - - + -
352A PHE* 4.3 17.9 - - + +
355A VAL* 3.8 40.2 - - + -
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Residues in contact with HIS 316 (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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39A ARG* 3.7 18.5 + - - +
55A GLU 3.4 23.3 - - - -
56A ALA* 4.4 2.2 - - - -
57A PRO* 4.4 6.7 - - + -
112A ASN* 3.0 42.1 + - - +
115A ALA* 3.3 13.8 - - - +
314A ASP* 2.7 24.7 + - - +
315A PRO* 1.3 82.8 - - + +
317A PHE* 1.3 62.0 + - + +
340A HIS 5.8 0.4 - - - -
341A SER* 6.0 2.9 - - - -
342A ASN 6.0 2.9 + - - -
344A HIS* 5.6 4.5 - + + -
348A SER* 2.8 40.9 + - - -
351A MSE 3.5 17.1 - - + +
352A PHE* 5.3 7.6 - + + -
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Residues in contact with PHE 317 (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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57A PRO* 4.9 1.1 - - + -
106A THR* 3.0 55.9 - - + +
107A PHE* 4.1 3.1 - - + -
109A LEU* 6.5 0.7 - - + -
111A VAL* 3.2 32.8 - - + +
112A ASN* 3.3 18.4 - - - -
290A ASN* 4.0 11.4 - - + -
294A THR* 5.1 9.6 - - + +
314A ASP* 2.9 29.6 + - + +
316A HIS* 1.3 84.1 - - + +
318A TRP* 1.3 71.2 + + + +
319A THR 3.5 0.7 - - - -
340A HIS* 3.1 35.0 - + + -
342A ASN* 3.5 15.7 - - - -
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Residues in contact with TRP 318 (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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89A HIS* 5.7 1.8 - - - -
290A ASN* 6.4 0.2 - - - +
293A ALA 3.2 20.7 + - - -
294A THR* 3.1 22.7 + - - +
295A ASN* 3.3 35.0 - - - -
296A TRP* 3.7 23.1 - + - -
299A MSE 3.5 23.3 - - + -
312A LEU 4.1 5.7 + - - -
313A ALA* 3.5 19.2 - - + +
314A ASP* 2.7 42.2 + - + +
317A PHE* 1.3 83.6 - - + +
319A THR* 1.3 79.2 + - - +
322A GLY* 3.1 11.5 - - - -
323A ALA* 3.7 15.7 - - + +
326A VAL* 3.6 23.3 - - + -
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Residues in contact with THR 319 (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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85A VAL* 5.4 2.0 - - + -
89A HIS* 4.5 21.6 - - + +
111A VAL* 4.6 5.4 - - + +
114A VAL* 4.5 11.2 - - + -
115A ALA* 3.8 27.3 - - + +
118A GLU* 3.8 16.6 + - - +
315A PRO 2.6 21.5 + - - -
317A PHE 3.5 3.0 - - - +
318A TRP* 1.3 85.3 + - - +
320A LEU* 1.3 56.0 + - - +
321A THR* 3.7 3.5 + - - -
322A GLY* 2.9 15.9 + - - -
323A ALA* 2.7 34.1 + - - +
325A ARG* 5.2 1.0 + - - -
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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