Contacts of the helix formed by residues 677 - 691 (chain B) in PDB entry 3N57
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 GLN 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LYS* 2.7 58.1 + - + +
196B ASN* 5.2 5.5 - - - +
676B GLU* 1.3 77.9 - - - +
678B PRO* 1.4 66.9 - - + +
679B HIS* 3.3 17.9 - - + -
680B GLN* 2.9 41.8 + - - +
681B HIS* 3.1 10.4 + - - -
783B ASN* 3.9 0.4 - - - -
786B HIS* 4.1 13.8 + - - -
851B GLN* 3.1 24.5 - - - +
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Residues in contact with PRO 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B GLN* 1.4 86.3 - - + +
679B HIS* 1.3 61.8 + - - +
681B HIS* 3.2 7.1 + - + +
682B ALA* 3.0 22.0 + - - +
783B ASN* 3.6 16.1 - - + +
786B HIS* 3.9 25.1 - - + -
788B ASN* 3.2 25.4 - - + +
789B SER 3.6 3.6 - - - +
790B GLY* 3.5 24.5 - - - +
851B GLN* 3.4 18.2 - - - +
958B VAL* 4.0 12.2 - - + +
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Residues in contact with HIS 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B GLN* 3.3 28.7 - - + +
678B PRO* 1.3 78.2 - - - +
680B GLN* 1.3 74.7 + - + +
682B ALA* 3.4 8.6 + - - +
683B MET* 3.1 46.1 + - + +
790B GLY* 4.1 5.5 - - - -
791B ILE 5.2 0.2 - - - +
832B ILE* 3.8 31.5 - - + +
849B ILE* 3.8 22.9 - - + +
850B ILE 4.5 2.2 - - - +
851B GLN* 2.9 37.1 + - + +
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Residues in contact with GLN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PHE* 4.3 5.9 - - + -
676B GLU* 3.1 32.4 + - + +
677B GLN* 2.9 49.9 + - - +
679B HIS* 1.3 92.9 + - + +
681B HIS* 1.3 62.0 + - - +
683B MET* 3.5 16.9 + - + +
684B TYR* 3.0 29.3 + - - +
687B ARG* 5.1 1.2 + - - -
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Residues in contact with HIS 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PHE* 2.9 49.7 + + - -
674B ARG* 4.0 11.9 - - - -
676B GLU* 3.8 7.7 + - + -
677B GLN 3.1 13.2 + - - -
678B PRO 3.3 8.7 - - - +
680B GLN* 1.3 74.9 - - - +
682B ALA* 1.3 55.8 + - - +
684B TYR* 3.0 7.2 + - - +
685B TYR* 2.8 66.1 + + + -
782B ARG 4.7 2.2 + - - -
783B ASN* 3.2 39.7 + - + +
784B GLU 5.4 0.2 - - - -
958B VAL* 4.0 11.5 - - + +
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Residues in contact with ALA 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B PRO 3.0 12.1 + - - +
679B HIS* 3.5 12.3 - - - +
680B GLN 3.3 0.2 - - - -
681B HIS* 1.3 77.2 - - - +
683B MET* 1.3 61.4 + - + +
685B TYR 3.4 0.2 + - - -
686B LEU* 3.1 24.3 + - - +
791B ILE* 4.2 8.5 - - - +
792B GLU* 3.9 29.7 - - + +
849B ILE* 5.9 0.4 - - + -
956B VAL* 3.7 15.1 - - + +
958B VAL* 3.7 18.5 - - + +
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Residues in contact with MET 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B HIS* 3.1 36.7 + - + +
680B GLN* 3.7 23.6 - - + +
682B ALA* 1.3 75.6 - - + +
684B TYR* 1.3 63.6 + - - +
686B LEU* 3.4 3.1 + - - +
687B ARG* 3.1 40.9 + - - +
792B GLU* 3.2 20.6 - - - +
838B ARG* 5.2 1.9 + - - -
847B ARG* 5.0 7.0 - - - +
849B ILE* 3.7 26.5 - - + -
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Residues in contact with TYR 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PHE* 3.4 34.3 - + + -
680B GLN 3.0 18.4 + - - +
681B HIS 3.4 3.1 - - - +
683B MET* 1.3 77.6 - - - +
685B TYR* 1.3 90.3 + + - +
687B ARG* 3.4 28.7 - - + +
688B LEU* 3.1 55.9 + - + +
695B TRP 5.5 1.1 - - - -
696B THR* 3.6 3.3 - - - -
697B LYS* 3.0 55.1 + - + +
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Residues in contact with TYR 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PHE* 5.4 1.8 - + - -
681B HIS* 2.8 57.7 + + + +
684B TYR* 1.3 99.5 - + - +
686B LEU* 1.3 57.2 + - - +
688B LEU* 3.3 6.9 + - + +
689B LEU* 2.9 32.6 + - - +
779B TYR* 3.9 17.0 - + + -
781B GLN* 3.2 40.9 - - + +
782B ARG 4.9 2.1 + - - -
956B VAL* 3.8 24.9 - - + -
958B VAL* 4.0 5.8 - - + -
995B MET* 4.0 18.6 - - + +
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Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B ALA 3.1 16.8 + - - +
683B MET 3.7 4.0 - - - +
684B TYR 3.3 0.2 - - - -
685B TYR* 1.3 74.0 - - - +
687B ARG* 1.3 59.1 + - - +
689B LEU* 3.0 5.5 + - + +
690B MET* 2.8 53.2 + - + +
792B GLU* 3.4 34.1 - - + +
794B TYR* 4.1 19.5 - - + -
838B ARG* 3.2 33.4 - - - +
954B VAL* 4.1 25.4 - - + +
956B VAL* 3.9 14.3 - - + +
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Residues in contact with ARG 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B PHE* 6.1 0.4 - - - -
680B GLN 5.1 1.0 + - - -
683B MET* 3.1 30.6 + - - +
684B TYR* 3.4 41.7 - - + +
686B LEU* 1.3 77.5 - - - +
688B LEU* 1.3 62.6 + - + +
690B MET 3.4 0.3 + - - -
691B THR* 2.6 35.7 + - - +
694B ALA* 4.8 1.5 - - - +
838B ARG* 4.3 16.3 - - - +
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Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B TYR* 3.1 54.5 + - + +
685B TYR* 3.5 8.5 - - + +
687B ARG* 1.3 80.4 - - + +
689B LEU* 1.3 57.0 + - - +
690B MET 3.7 0.2 + - - -
691B THR 4.0 2.3 - - - +
694B ALA* 3.9 23.6 - - + +
695B TRP 3.8 26.7 - - - +
696B THR* 3.7 19.5 - - + -
995B MET* 3.8 23.7 - - + +
999B LYS* 2.9 31.5 + - - -
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Residues in contact with LEU 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B TYR 2.9 17.7 + - - +
686B LEU* 3.0 6.0 + - - +
688B LEU* 1.3 79.0 - - - +
690B MET* 1.3 73.3 + - + +
691B THR 3.6 0.2 - - - -
769B VAL* 3.8 7.4 - - - +
779B TYR* 3.6 32.1 - - + -
954B VAL* 4.5 8.7 - - + -
956B VAL* 4.4 13.9 - - + -
992B ILE* 3.9 31.0 - - + -
995B MET* 3.5 33.0 - - + -
998B PHE* 3.5 29.2 - - + -
999B LYS* 4.0 5.9 - - - +
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Residues in contact with MET 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B LEU* 2.8 33.1 + - + +
687B ARG 4.5 0.9 - - - +
689B LEU* 1.3 107.2 - - + +
691B THR* 1.3 58.7 + - - +
768B GLU* 3.2 43.3 - - - +
769B VAL* 3.3 25.7 + - + +
771B LEU* 4.2 9.9 - - + -
794B TYR* 4.4 14.8 - - + -
796B GLN* 4.9 0.7 - - - +
838B ARG* 4.1 7.4 - - - +
841B ASN* 4.4 1.3 + - - -
954B VAL* 4.1 28.7 - - + -
998B PHE* 3.5 28.3 - - + -
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Residues in contact with THR 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ILE* 5.5 6.5 - - + -
687B ARG* 2.6 31.6 + - - +
688B LEU 4.0 0.5 + - - +
689B LEU 3.6 0.4 - - - -
690B MET* 1.3 79.4 - - - +
692B GLU* 1.3 73.2 + - - +
693B VAL* 3.2 18.4 + - - +
694B ALA* 4.4 6.9 - - + +
766B TYR* 4.2 14.1 - - + -
767B ARG 3.8 1.3 - - - +
769B VAL* 4.9 1.1 - - - -
838B ARG* 5.7 1.2 + - - -
841B ASN* 4.0 28.4 + - - +
999B LYS* 3.2 22.3 + - - -
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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
------------------------------------------------------------
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