Contacts of the helix formed by residues 658 - 662 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.0 46.5 + - - +
245A SER* 4.1 15.0 + - - +
247A GLN* 6.1 1.0 - - - +
656B VAL* 4.4 3.3 - - - +
657B SER* 1.3 82.0 + - - +
659B TRP* 1.3 59.6 + - - +
660B GLU* 3.4 39.4 + - - +
661B TYR* 2.8 69.4 + - + +
662B TYR 4.0 1.0 + - - -
683B TYR 4.9 1.1 - - - +
684B ARG* 3.5 27.3 - - - +
686B SER 5.0 0.7 - - - -
687B THR* 3.4 25.8 - - + +
689B MET* 3.9 3.1 - - + -
715B GLN* 3.5 3.3 - - - +
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Residues in contact with TRP 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ALA* 3.6 4.7 - - - +
598B LEU* 3.6 20.4 - - + +
631B TYR* 3.6 37.9 - + - -
634B TYR* 3.4 33.0 + + - -
656B VAL* 3.8 23.3 - - + -
658B ARG* 1.3 67.2 - - - +
660B GLU* 1.3 60.1 + - - +
661B TYR 2.9 6.6 + - - -
662B TYR* 3.2 42.8 + + + +
666B TYR* 4.1 9.9 - + - -
667B THR* 3.6 40.0 - - + +
671B MET* 3.9 14.1 - - + -
683B TYR* 3.7 21.5 + - + +
686B SER* 3.8 23.6 - - - -
955B A3M 4.0 6.7 - - + -
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Residues in contact with GLU 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN* 3.0 38.7 - - + +
258B LYS* 3.5 5.4 - - - +
259B ALA* 3.9 6.9 + - + -
658B ARG* 3.0 27.6 + - - +
659B TRP* 1.3 77.5 - - - +
661B TYR* 1.3 60.4 + - + +
662B TYR 3.5 0.7 - - - -
674B PRO* 4.0 14.5 - - + +
680B LEU* 4.1 10.7 - - - +
683B TYR* 3.8 27.4 + - + +
684B ARG* 2.8 48.3 + - - -
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Residues in contact with TYR 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 2.6 29.0 + - - +
246A LEU 3.6 12.1 - - - -
247A GLN* 3.8 9.6 - - - -
256B TYR* 4.3 4.2 + - - -
258B LYS* 3.1 26.6 + - - +
657B SER* 3.4 22.2 - - - -
658B ARG* 2.8 43.3 + - + +
660B GLU* 1.3 80.2 - - - +
662B TYR* 1.3 63.3 + - - +
689B MET* 3.7 6.7 - - + -
712B HIS* 4.3 1.0 - - - -
714B GLN* 3.5 31.4 - - + +
715B GLN* 3.3 29.4 + - + +
718B GLN* 3.2 30.6 + - + +
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Residues in contact with TYR 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 2.9 18.9 + - - -
256B TYR* 3.6 10.8 - - - -
258B LYS* 3.3 1.8 - - - -
259B ALA 2.9 22.9 + - - -
656B VAL* 4.3 4.9 - - + -
658B ARG 4.0 0.8 + - - +
659B TRP* 3.2 27.3 + + + +
661B TYR* 1.3 82.4 - - - +
663B ASP* 1.3 80.6 + - - +
666B TYR* 3.5 17.5 - + + -
667B THR* 3.2 23.7 + - - +
710B ASN* 2.6 41.1 + - - -
711B VAL* 3.7 18.6 - - + -
715B GLN* 3.8 10.0 - - - +
955B A3M 2.9 34.0 + - - -
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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
------------------------------------------------------------
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