Contacts of the helix formed by residues 688 - 698 (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 VAL 688 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634B TYR* 4.0 10.8 - - + -
637B SER* 3.7 35.0 - - - -
638B MET* 4.1 9.2 - - - -
656B VAL 3.5 24.7 - - - +
657B SER* 2.7 18.8 + - - +
687B THR* 1.3 73.8 - - - +
689B MET* 1.3 65.1 + - - +
691B ARG* 3.0 20.9 + - - +
692B ALA* 3.9 2.9 + - - -
695B PHE* 4.2 16.6 - - + -
719B ILE* 3.8 28.3 - - + -
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Residues in contact with MET 689 (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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244A GLU* 3.3 37.5 - - + +
657B SER* 3.1 46.4 - - - +
658B ARG* 3.9 8.5 - - + -
661B TYR* 3.7 20.2 - - + -
687B THR* 4.1 2.5 - - - +
688B VAL* 1.3 74.7 - - - +
690B SER* 1.3 56.5 + - - +
691B ARG 2.9 10.9 + - - -
692B ALA* 3.1 19.7 + - - +
718B GLN* 3.7 29.2 - - + +
719B ILE* 3.9 5.8 - - - +
722B ALA* 3.5 25.3 - - + +
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Residues in contact with SER 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 5.2 0.8 + - - -
684B ARG 4.6 8.1 - - - -
685B ASN* 4.5 8.0 + - - -
687B THR* 3.1 32.8 + - - -
688B VAL 3.2 0.2 + - - -
689B MET* 1.3 75.8 - - - +
691B ARG* 1.3 68.3 + - - +
692B ALA 3.6 0.4 - - - -
693B GLU* 5.5 0.7 + - - +
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Residues in contact with ARG 691 (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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599B GLY 5.3 1.8 + - - -
603B VAL* 4.6 7.9 - - - +
638B MET* 3.1 60.7 + - - +
641B GLY* 3.2 25.4 + - - +
642B SER* 4.3 11.7 - - - +
685B ASN 4.6 9.5 + - - -
687B THR 3.6 23.3 - - - -
688B VAL* 3.0 9.9 + - - +
689B MET 2.9 1.0 - - - -
690B SER* 1.3 88.5 + - - +
692B ALA* 1.3 64.2 + - - +
693B GLU* 3.2 3.4 - - - -
694B ASN* 3.2 23.2 + - - +
695B PHE* 3.3 12.7 - - + -
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Residues in contact with ALA 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B VAL 3.9 0.6 + - - -
689B MET* 3.1 18.6 + - - +
690B SER 3.6 1.0 - - - -
691B ARG* 1.3 76.4 - - - +
693B GLU* 1.3 64.0 + - - +
695B PHE* 2.9 32.0 + - - +
722B ALA* 3.8 20.0 - - + +
723B LEU* 3.7 12.9 - - + +
726B VAL* 3.7 23.6 - - + -
728B VAL* 4.0 4.5 - - - +
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Residues in contact with GLU 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B SER 5.5 1.1 + - - +
691B ARG* 3.2 1.1 + - - -
692B ALA* 1.3 78.7 - - - +
694B ASN* 1.3 64.5 + - - +
695B PHE 2.9 5.4 + - - -
696B LYS* 3.2 53.6 + - - +
697B GLN* 5.2 0.7 + - - -
726B VAL* 4.0 29.6 - - + +
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Residues in contact with ASN 694 (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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640B LEU 4.2 6.2 - - - +
641B GLY 3.5 29.2 + - - +
642B SER 4.2 3.4 + - - -
643B GLY* 3.8 25.8 - - - +
691B ARG* 3.2 16.9 + - - +
693B GLU* 1.3 80.8 - - - +
695B PHE* 1.3 56.9 + - - +
696B LYS 3.0 7.1 + - - -
697B GLN* 3.1 34.8 - - - +
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Residues in contact with PHE 695 (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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637B SER* 3.4 29.4 - - - -
640B LEU* 3.7 16.2 - - + -
641B GLY* 3.8 14.6 - - - -
688B VAL* 4.2 21.8 - - + -
691B ARG* 3.3 24.9 - - + -
692B ALA* 2.9 16.3 + - - +
694B ASN* 1.3 76.6 - - - +
696B LYS* 1.3 59.6 + - - +
697B GLN 3.2 0.9 - - - -
698B VAL* 3.4 29.9 - - + +
700B TYR* 3.7 48.8 - + + +
719B ILE* 6.0 0.2 - - + -
723B LEU* 3.5 22.9 - - + -
728B VAL* 3.4 15.2 - - + +
729B ASP 4.9 0.2 - - - +
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Residues in contact with LYS 696 (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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693B GLU* 3.2 35.9 + - - +
694B ASN 3.0 2.2 + - - -
695B PHE* 1.3 78.4 - - - +
697B GLN* 1.3 63.7 + - + +
698B VAL 3.4 2.9 + - - +
726B VAL 4.7 8.8 + - - +
727B GLY 4.8 8.3 + - - -
728B VAL* 4.1 23.6 - - + -
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Residues in contact with GLN 697 (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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640B LEU 5.7 0.2 - - - +
643B GLY* 4.4 23.6 - - - +
645B GLY* 5.2 6.0 + - - -
647B PHE 4.7 2.4 - - - +
648B LYS* 4.9 1.0 - - - +
693B GLU 5.2 1.0 + - - -
694B ASN* 3.1 33.5 + - - +
695B PHE 3.2 0.2 - - - -
696B LYS* 1.3 81.6 - - - +
698B VAL* 1.3 70.8 + - + +
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Residues in contact with VAL 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B LEU* 4.0 52.3 - - + +
645B GLY* 6.4 2.0 - - - -
647B PHE* 3.7 18.2 - - + +
648B LYS 3.7 9.4 - - - +
695B PHE* 3.4 30.2 - - + +
696B LYS 3.4 3.5 + - - +
697B GLN* 1.3 90.4 - - + +
699B GLU* 1.3 68.3 + - - +
700B TYR* 3.6 3.3 + - + +
729B ASP 5.1 4.5 - - - +
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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