Contacts of the helix formed by residues 603 - 618 (chain B) in PDB entry 7NPA
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 GLY 603 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B MET 2.8 11.0 + - - +
600B ALA* 3.9 4.5 + - - -
601B ARG 3.5 2.4 - - - -
602B ILE* 1.3 79.4 - - - +
604B LYS* 1.3 66.3 + - - -
605B GLY 3.3 3.1 - - - -
606B LYS* 3.3 4.9 + - - -
607B PHE* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 6.0 7.0 - - - +
560B GLU 5.7 3.7 + - - -
562B VAL* 4.2 22.0 - - + +
596B ALA 6.2 0.2 - - - -
599B MET* 3.4 38.5 + - + +
600B ALA* 5.0 10.8 - - - +
603B GLY* 1.3 71.3 - - - -
605B GLY* 1.3 58.5 + - - +
607B PHE* 3.3 2.1 + - - +
608B LEU* 2.9 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLY 3.3 0.4 - - - -
604B LYS* 1.3 77.1 - - - +
606B LYS* 1.3 64.8 + - - +
608B LEU* 4.2 4.7 - - - +
609B GLU* 2.9 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B TYR* 3.7 31.5 + - - -
602B ILE* 3.5 36.5 - - + +
603B GLY* 3.3 4.4 + - - +
605B GLY* 1.3 75.9 - - - +
607B PHE* 1.3 64.1 + - - +
609B GLU* 3.4 10.9 + - - +
610B GLU* 3.1 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B VAL* 5.3 0.4 - - + -
579B VAL* 3.8 13.5 - - + -
582B VAL* 3.5 24.0 - - + +
583B TYR* 3.7 25.8 - - - -
595B LEU* 3.4 32.3 - - + -
598B VAL* 4.0 13.7 - - + -
599B MET* 3.6 28.5 - - + -
602B ILE* 3.7 23.5 - - + +
603B GLY 3.0 16.5 + - - +
604B LYS 3.7 3.8 - - - +
606B LYS* 1.3 78.0 - - - +
608B LEU* 1.3 69.4 + - + +
610B GLU* 3.2 7.1 + - - +
611B VAL* 3.1 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B VAL* 4.0 27.6 - - + -
562B VAL* 4.0 35.0 - - + -
564B MET* 4.0 29.0 - - + +
575B LEU* 5.9 0.4 - - + -
579B VAL* 5.7 0.2 - - + -
599B MET* 4.2 9.2 - - + -
604B LYS* 2.9 23.5 + - + +
605B GLY* 4.2 3.8 - - - +
607B PHE* 1.3 81.1 - - + +
609B GLU* 1.3 60.3 + - - +
611B VAL* 3.2 11.7 + - + +
612B LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B GLY* 2.9 31.4 + - - +
606B LYS* 3.7 9.5 - - - +
608B LEU* 1.3 77.8 - - - +
610B GLU* 1.3 62.9 + - + +
612B LYS* 3.3 8.2 + - - +
613B GLU* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B VAL* 4.3 14.9 - - + +
585B LYS* 2.9 29.5 + - - +
586B TYR* 2.5 37.4 + - - -
606B LYS* 3.1 26.0 + - + +
607B PHE 3.7 7.2 - - - +
609B GLU* 1.3 76.8 - - + +
611B VAL* 1.3 65.8 + - - +
613B GLU* 3.3 21.6 + - - +
614B LEU* 3.1 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B MET* 6.3 0.7 - - + -
575B LEU* 3.8 28.5 - - + -
578B LYS* 4.0 11.8 - - + +
579B VAL* 4.0 19.1 - - + -
582B VAL* 3.8 17.5 - - + -
607B PHE* 3.1 41.3 + - + +
608B LEU* 3.2 12.5 + - + +
610B GLU* 1.3 75.9 - - - +
612B LYS* 1.3 56.5 + - - +
614B LEU* 3.2 5.1 + - - +
615B MET* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LYS* 4.8 17.0 - - - +
608B LEU 2.9 16.6 + - - +
609B GLU* 3.5 8.5 - - - +
611B VAL* 1.3 76.0 - - - +
613B GLU* 1.3 63.6 + - + +
615B MET* 3.2 17.9 + - + +
616B GLU* 3.0 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLU* 3.0 30.1 + - - +
610B GLU* 3.3 24.2 + - - +
612B LYS* 1.3 76.6 - - + +
614B LEU* 1.3 62.9 + - + +
616B GLU* 3.2 15.7 + - - +
617B GLN* 3.2 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B LYS* 3.6 30.3 - - + +
581B ILE* 3.8 27.6 - - + -
582B VAL* 3.7 26.7 - - + -
610B GLU* 3.1 15.5 + - + +
611B VAL 3.7 6.3 - - - +
613B GLU* 1.3 78.1 - - + +
615B MET* 1.3 61.8 + - - +
617B GLN* 3.3 29.6 + - - +
618B ASN 3.2 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B MET* 5.2 7.0 - - + -
571B GLU* 3.5 35.9 - - + +
574B ASN* 3.0 30.3 + - + +
575B LEU* 3.7 33.0 - - + +
578B LYS* 3.7 16.6 - - + -
611B VAL* 2.9 22.2 + - - +
612B LYS* 3.2 19.0 + - + +
614B LEU* 1.3 78.1 - - - +
616B GLU* 1.3 57.8 + - + +
618B ASN* 3.0 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B LYS* 3.0 51.3 + - + +
613B GLU* 3.2 16.4 + - - +
615B MET* 1.3 75.9 - - + +
617B GLN* 1.3 65.0 + - - +
618B ASN* 3.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B GLU* 3.2 22.1 + - - +
614B LEU* 3.3 29.4 + - - +
616B GLU* 1.3 75.4 - - + +
618B ASN* 1.3 65.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ASN* 3.3 33.0 - - - +
578B LYS* 3.0 19.0 + - - +
614B LEU 3.2 8.3 + - - +
615B MET 3.0 19.3 - - - +
616B GLU 3.2 3.0 - - - -
617B GLN* 1.3 81.9 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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