Contacts of the helix formed by residues 658 - 662 (chain A) in PDB entry 1N1M
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 ARG 658 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A VAL* 4.2 2.9 - - - +
657A SER* 1.3 85.0 + - - +
659A TRP* 1.3 58.9 + - - +
660A GLU* 3.5 40.8 + - - +
661A TYR* 2.8 71.4 + - + +
662A TYR 4.0 0.9 + - - -
683A TYR 5.4 0.4 - - - +
684A ARG* 3.7 25.6 - - - +
686A SER 5.3 0.9 - - - -
687A THR* 3.5 21.3 - - + +
689A MET* 3.5 7.0 - - + -
715A GLN* 3.3 3.5 + - - +
244B GLU* 2.9 49.0 + - - +
245B SER* 3.9 16.8 + - - +
246B LEU 5.7 0.2 - - - -
247B GLN* 6.1 0.6 - - - +
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Residues in contact with TRP 659 (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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259A ALA* 3.7 3.6 - - - +
598A LEU* 3.8 20.2 - - + +
631A TYR* 3.5 39.3 - + - -
634A TYR* 3.1 40.6 + + - -
656A VAL* 3.8 31.9 - - + -
658A ARG* 1.3 70.9 - - - +
660A GLU* 1.3 61.3 + - - +
661A TYR 3.0 1.8 + - - -
662A TYR* 3.0 26.5 + + + +
666A TYR* 4.2 11.9 - + - -
667A THR* 3.6 40.3 - - + +
671A MET* 4.1 11.4 - - + -
683A TYR* 3.8 21.9 + - + +
686A SER* 3.7 24.2 - - - +
954A A3M 4.1 8.1 - - + -
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Residues in contact with GLU 660 (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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258A LYS* 3.5 8.7 - - - +
259A ALA* 3.8 9.0 + - - -
658A ARG* 3.0 28.4 + - - +
659A TRP* 1.3 76.7 - - - +
661A TYR* 1.3 61.3 + - + +
662A TYR 3.4 1.1 - - - -
674A PRO* 4.1 13.9 - - + +
680A LEU* 4.3 5.3 - - - +
683A TYR* 3.5 33.5 - - + +
684A ARG* 2.8 50.4 + - - -
247B GLN* 2.8 36.5 - - + +
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Residues in contact with TYR 661 (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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256A TYR* 4.3 4.2 + - - -
258A LYS* 2.7 29.5 + - - +
657A SER* 3.5 20.9 - - - -
658A ARG* 2.8 42.5 + - + +
660A GLU* 1.3 80.8 - - + +
662A TYR* 1.3 60.4 + - - +
689A MET* 3.7 4.5 - - + -
710A ASN 5.5 0.2 - - - +
712A HIS* 4.3 1.9 + - - -
714A GLN* 3.5 30.5 - - + +
715A GLN* 3.4 23.3 + - + +
718A GLN* 3.3 30.8 + - + +
244B GLU* 2.5 28.8 + - - +
246B LEU 3.2 22.8 + - - -
247B GLN* 3.9 8.1 - - - -
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Residues in contact with TYR 662 (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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206A GLU* 3.1 9.2 + - - -
256A TYR* 3.4 14.8 - - - -
258A LYS* 3.3 2.4 - - - -
259A ALA 2.8 25.3 + - - -
656A VAL* 4.7 1.1 - - + -
659A TRP* 3.0 25.9 + + + +
661A TYR* 1.3 79.8 - - - +
663A ASP* 1.3 86.7 + - - +
666A TYR* 3.6 20.9 - + + -
667A THR* 3.3 20.6 - - - +
710A ASN* 2.5 39.8 + - - -
711A VAL* 4.0 6.5 - - + -
715A GLN* 3.8 14.7 - - - +
954A A3M 2.8 48.7 + - + -
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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