Contacts of the helix formed by residues 625 - 637 (chain D) in PDB entry 5NPK
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 625 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619D GLU 5.6 2.0 + - - +
620D MET 4.6 2.8 - - - +
623D GLY 3.4 1.6 - - - -
624D ASP* 1.3 90.1 + - - +
626D VAL* 1.3 64.4 + - - +
627D GLU* 3.4 10.5 + - + +
628D ASN* 3.5 32.7 + - + +
629D ARG* 3.7 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 626 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624D ASP 3.2 9.3 + - - +
625D VAL* 1.3 73.1 - - - +
627D GLU* 1.4 59.4 + - - +
629D ARG* 3.1 27.7 + - - +
630D ARG* 2.8 24.9 + - - +
1178D GLY* 3.7 33.4 - - - +
1179D MET* 4.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D VAL* 3.3 7.9 - - + +
626D VAL* 1.4 81.7 - - - +
628D ASN* 1.3 62.2 + - - +
630D ARG* 2.6 44.3 + - - +
631D GLN* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 628 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D MET* 4.0 21.5 - - + +
625D VAL* 3.5 29.4 + - + +
626D VAL 3.4 0.2 - - - -
627D GLU* 1.3 82.8 - - - +
629D ARG* 1.3 60.9 + - - +
631D GLN* 3.4 7.6 + - - +
632D PHE* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 629 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D LYS* 3.7 20.1 - - - +
620D MET* 3.5 25.0 + - - +
621D LEU* 3.0 30.9 + - + +
622D MET 3.9 1.2 - - - -
623D GLY 2.7 31.3 + - - +
624D ASP 4.3 1.4 - - - -
625D VAL 3.7 6.4 + - - +
626D VAL* 3.1 38.5 + - - +
628D ASN* 1.3 74.6 - - - +
630D ARG* 1.3 65.1 + - - +
632D PHE* 3.3 9.0 + - + +
633D ILE* 3.1 29.9 + - + +
1022D PHE* 3.5 29.4 - - + -
1177D VAL* 4.0 11.5 - - + +
1178D GLY* 4.6 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626D VAL 2.8 10.9 + - - +
627D GLU* 2.6 44.2 + - - +
629D ARG* 1.3 78.1 - - - +
631D GLN* 1.3 86.4 + - - +
633D ILE* 3.2 8.8 + - + +
634D GLU* 2.9 52.2 + - + +
1178D GLY* 3.3 33.4 - - - +
1179D MET* 3.9 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 631 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627D GLU* 2.9 20.4 + - + +
628D ASN* 3.7 9.4 - - - +
630D ARG* 1.3 97.4 + - - +
632D PHE* 1.3 63.3 + - - +
634D GLU* 3.4 18.6 + - - +
635D ASP* 2.9 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 632 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D MET* 3.9 18.2 - - + -
621D LEU* 3.5 24.5 - - + -
628D ASN 3.1 14.6 + - - +
629D ARG* 3.5 9.0 - - - +
630D ARG 3.2 0.2 - - - -
631D GLN* 1.3 77.4 - - - +
633D ILE* 1.3 71.3 + - + +
635D ASP* 3.3 3.0 + - - -
636D ASN* 3.0 60.0 + - + +
1019D ARG* 3.6 63.5 - - + -
1022D PHE* 4.9 2.2 - + - -
1023D LEU* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D ARG* 3.1 26.0 + - + +
630D ARG* 3.2 11.2 + - + +
632D PHE* 1.3 84.8 - - + +
634D GLU* 1.3 63.4 + - - +
636D ASN 3.7 0.3 - - - -
637D ALA* 3.0 24.1 + - - +
1022D PHE* 4.8 1.1 - - + -
1023D LEU* 4.0 9.1 - - + +
1026D ALA* 3.4 29.4 - - + -
1027D MET* 3.8 30.5 - - + -
1030D ILE* 3.9 15.3 - - + -
1177D VAL* 4.0 28.5 - - + +
1178D GLY* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D ARG* 2.9 42.9 + - - +
631D GLN* 3.5 19.0 + - - +
633D ILE* 1.3 79.1 - - - +
635D ASP* 1.3 65.6 + - - +
636D ASN 3.4 0.2 + - - -
637D ALA* 3.6 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D GLN* 2.9 51.1 + - - +
632D PHE* 3.8 2.1 - - - +
634D GLU* 1.3 80.6 - - - +
636D ASN* 1.3 72.8 + - - +
637D ALA 3.5 0.6 + - - -
638D VAL* 5.2 1.2 + - - +
639D TYR* 4.4 8.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D PHE* 3.0 50.0 + - + +
633D ILE 3.7 1.6 - - - -
635D ASP* 1.3 86.9 - - - +
637D ALA* 1.3 64.5 + - - +
638D VAL 3.1 3.1 - - - -
639D TYR* 3.0 35.7 + - + -
1019D ARG* 5.7 0.2 - - - +
1023D LEU* 3.1 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 637 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D ILE 3.0 16.4 + - - +
634D GLU* 3.6 11.6 + - - +
635D ASP 3.5 2.6 - - - -
636D ASN* 1.3 77.6 - - - +
638D VAL* 1.3 63.7 + - + +
640D ALA* 3.2 18.4 + - - +
1027D MET* 3.6 35.6 - - + +
----------------------------------------------------------
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