Contacts of the helix formed by residues 314 - 320 (chain B) in PDB entry 4NH1
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 THR 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 3.6 20.0 - - + +
11B VAL* 3.6 33.3 - - + +
12B TYR* 6.5 0.4 - - - -
215B MET* 3.8 5.4 - - - -
312B ARG 4.4 1.1 - - - +
313B LEU* 1.3 77.2 - - - +
315B ALA* 1.3 58.3 + - - +
316B ARG* 3.5 6.3 + - - +
317B GLU* 3.1 39.8 + - - +
318B ALA* 2.8 27.9 + - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.6 23.1 - - + +
144B LEU* 4.2 4.7 - - + -
145B ASP* 3.4 39.2 + - + +
148B HIS* 4.5 8.5 + - + +
215B MET* 3.9 14.7 - - - +
314B THR* 1.3 74.2 - - - +
316B ARG* 1.3 63.0 + - - +
318B ALA 3.5 0.2 + - - -
319B MET* 3.2 27.6 + - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 6.1 3.4 - - + -
12B TYR* 4.8 4.7 - - - +
138B TYR* 5.2 0.8 + - - -
145B ASP* 3.0 26.9 + - - +
314B THR* 3.3 5.5 + - - +
315B ALA* 1.3 73.0 - - - +
317B GLU* 1.3 66.8 + - + +
319B MET* 3.2 42.1 + - - +
320B GLU* 3.3 41.3 + - + +
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ARG* 2.7 33.4 + - - -
11B VAL* 5.8 0.4 - - - -
313B LEU* 3.7 24.2 - - + +
314B THR* 3.1 33.9 + - - +
316B ARG* 1.3 77.0 - - + +
318B ALA* 1.3 63.0 + - - +
320B GLU* 3.2 25.3 + - - +
321B HIS* 4.6 1.9 - - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.7 24.5 - - + -
215B MET* 4.2 6.7 - - + -
300B PHE* 3.5 25.6 - - + -
313B LEU* 4.0 11.0 - - + +
314B THR 2.8 18.2 + - - +
315B ALA 3.7 0.2 - - - +
317B GLU* 1.3 78.3 - - - +
319B MET* 1.3 61.8 + - - +
321B HIS* 3.2 19.6 - - - +
324B PHE* 3.3 11.6 - - - -
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Residues in contact with MET 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TYR* 3.2 53.5 - - + +
141B LEU* 3.7 36.6 - - + +
142B LYS* 4.3 13.7 - - + -
145B ASP* 4.6 5.6 - - - -
315B ALA 3.2 16.4 + - - +
316B ARG* 3.2 41.5 + - - +
318B ALA* 1.3 77.1 - - - +
320B GLU* 1.3 61.7 + - + +
321B HIS 3.2 5.2 + - - +
324B PHE* 4.0 14.8 - - - +
325B TYR* 6.1 0.2 - - - -
328B VAL* 4.7 3.1 - - - +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ARG* 3.3 47.1 + - + +
317B GLU* 3.2 16.3 + - - +
318B ALA 3.2 0.8 - - - -
319B MET* 1.3 77.8 - - - +
321B HIS* 1.3 59.4 + - - +
322B PRO* 4.5 2.1 - - - +
325B TYR* 5.2 7.6 + - - -
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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