Contacts of the helix formed by residues 307 - 311 (chain A) in PDB entry 3NSH
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 LEU 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A VAL* 3.8 23.3 - - + -
305A THR* 4.1 1.5 + - + -
306A ILE* 1.3 75.2 - - - +
308A PRO* 1.3 66.6 - - + +
309A GLN* 3.1 15.5 - - - +
310A GLN* 2.7 41.8 + - - +
311A TYR* 3.5 7.9 + - - -
367A VAL* 3.8 31.4 - - + +
369A ASP* 3.9 19.7 - - + +
372A ARG* 4.0 18.4 - - + +
373A THR 3.9 7.6 - - - +
374A ALA* 3.8 28.9 - - - +
217C GLN* 5.1 0.7 - - - +
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Residues in contact with PRO 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 3.8 15.7 - - + +
286A PHE* 3.2 48.7 - - + +
287A PRO 3.6 10.3 - - - +
288A VAL* 4.6 1.1 - - + -
307A LEU* 1.3 89.4 - - + +
309A GLN* 1.3 63.1 + - - +
310A GLN 2.9 0.4 - - - -
311A TYR* 3.6 18.3 - - + -
312A LEU* 2.9 35.3 + - + +
372A ARG* 3.7 20.9 - - - +
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Residues in contact with GLN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 3.4 53.7 - - + +
307A LEU* 3.0 21.7 + - + +
308A PRO* 1.3 80.0 - - - +
310A GLN* 1.3 60.0 + - - +
312A LEU 4.3 8.0 - - - +
313A ARG* 5.5 0.3 - - - -
314A PRO* 5.3 5.0 - - - +
345A GLU* 5.2 2.6 - - - +
367A VAL* 4.6 20.9 - - + +
368A HIS 3.4 24.0 + - - +
369A ASP* 2.9 27.6 + - - +
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Residues in contact with GLN 310 (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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305A THR 4.3 0.2 - - - +
306A ILE* 3.5 20.7 - - + +
307A LEU 2.7 38.4 + - - +
309A GLN* 1.3 75.3 - - - +
311A TYR* 1.3 60.8 + - - +
312A LEU 3.4 1.5 + - - -
313A ARG* 4.6 3.6 + - - +
329A ALA* 4.4 0.9 - - - +
342A VAL* 3.2 53.0 + - - +
343A ILE 3.4 13.3 + - - -
345A GLU* 3.2 30.0 + - - +
347A PHE* 3.8 10.7 - - - -
367A VAL* 3.7 34.7 - - + +
374A ALA* 4.3 6.0 - - - +
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Residues in contact with TYR 311 (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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240A LEU* 5.8 1.6 - - + -
254A ILE* 4.1 10.1 - - + +
286A PHE* 3.6 8.1 - + - +
287A PRO* 2.7 50.2 + - - +
289A ILE* 3.7 29.4 - - + -
306A ILE* 4.2 12.3 - - + -
307A LEU 3.5 9.8 + - - -
308A PRO* 3.6 19.7 - - + -
310A GLN* 1.3 79.0 - - - +
312A LEU* 1.3 73.9 + - + +
313A ARG 3.7 1.3 - - - -
328A PHE* 3.8 12.2 - + - -
329A ALA* 2.7 35.6 + - + +
330A ILE* 3.9 26.2 - - + -
342A VAL* 4.8 4.3 - - + -
343A ILE* 5.8 2.9 - - + -
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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