Contacts of the helix formed by residues 625 - 637 (chain U) in PDB entry 6QX2
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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619U GLU* 5.3 8.2 + - + +
620U MET* 4.4 2.8 - - - +
623U GLY* 3.3 2.2 - - - +
624U ASP* 1.3 76.8 - - + +
626U VAL* 1.3 63.5 + - - +
627U GLU* 3.6 11.2 + - + +
628U ASN* 3.3 35.2 + - - +
629U ARG* 3.8 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 626 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178T GLY* 3.1 36.6 - - - +
624U ASP 3.4 8.2 + - - +
625U VAL* 1.3 71.6 - - - +
627U GLU* 1.3 61.4 + - - +
629U ARG* 3.3 23.2 + - - +
630U ARG* 2.9 26.0 + - - +
2017V G 3.9 21.1 - - + +
2018V C 3.5 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625U VAL* 3.4 9.2 - - + +
626U VAL* 1.3 79.5 - - - +
628U ASN* 1.3 61.2 + - - +
630U ARG* 3.1 43.6 + - - +
631U GLN* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 628 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620U MET* 3.9 25.8 - - + +
625U VAL* 3.3 33.1 + - - +
626U VAL 3.4 0.4 - - - -
627U GLU* 1.3 79.6 - - - +
629U ARG* 1.3 57.1 + - - +
631U GLN* 3.5 8.0 + - - +
632U PHE* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 629 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T PHE* 3.6 27.4 - - + -
177T VAL* 3.9 4.0 - - - -
178T GLY* 4.5 1.1 - - - -
466U LYS* 3.8 7.2 - - - +
620U MET* 3.5 24.8 + - - +
621U LEU* 2.8 42.1 + - + +
622U MET 4.0 0.8 - - - -
623U GLY 2.8 31.3 + - - +
624U ASP 4.1 2.4 + - - -
625U VAL 3.8 5.4 + - - +
626U VAL* 3.3 30.8 + - - +
628U ASN* 1.3 74.8 - - - +
630U ARG* 1.3 63.6 + - - +
632U PHE* 3.4 9.3 + - - +
633U ILE* 3.2 34.0 + - + +
2016V C 5.1 0.4 - - - -
2017V G 2.9 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178T GLY* 3.5 26.4 - - - +
179T MET* 4.0 10.3 - - + -
626U VAL 2.9 13.1 + - - +
627U GLU* 3.1 33.1 + - - +
629U ARG* 1.3 72.5 - - - +
631U GLN* 1.3 98.6 + - - +
633U ILE* 3.2 14.0 + - - +
634U GLU* 2.9 53.5 + - - +
701U JK8 3.1 53.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 631 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627U GLU* 2.9 23.9 + - - +
628U ASN* 3.5 9.2 - - - +
629U ARG 3.3 0.2 - - - -
630U ARG* 1.3 101.1 + - - +
632U PHE* 1.3 55.1 + - - +
634U GLU* 3.3 13.1 + - - +
635U ASP* 2.9 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 632 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T ARG* 3.5 56.8 - - + -
22T PHE* 4.8 3.1 - + - -
23T LEU* 4.1 26.2 - - + -
620U MET* 3.7 25.8 - - + -
621U LEU* 3.3 27.4 - - + -
628U ASN 3.0 13.8 + - - +
629U ARG* 3.4 12.3 - - - +
631U GLN* 1.3 74.7 - - - +
633U ILE* 1.3 63.5 + - + +
635U ASP* 4.5 4.3 - - - -
636U ASN* 2.9 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22T PHE* 5.2 0.9 - - + -
23T LEU* 4.1 10.2 - - + +
26T ALA* 3.8 24.7 - - + -
27T MET* 3.8 22.7 - - + -
30T ILE* 3.7 20.4 - - + -
177T VAL* 3.7 32.8 - - + +
178T GLY* 4.4 0.2 - - - -
179T MET* 5.8 0.4 - - + -
629U ARG* 3.2 24.6 + - + +
630U ARG* 3.2 10.1 + - + +
632U PHE* 1.3 81.3 - - + +
634U GLU* 1.3 56.7 + - - +
636U ASN 3.3 1.6 + - - -
637U ALA* 2.8 34.7 + - - +
701U JK8 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 634 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630U ARG* 2.9 40.5 + - - +
631U GLN* 3.7 18.0 + - - +
633U ILE* 1.3 76.4 - - - +
635U ASP* 1.3 67.2 + - - +
637U ALA 3.4 3.6 + - - +
701U JK8 3.2 83.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 635 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631U GLN* 2.9 54.6 + - - +
632U PHE* 3.7 2.6 + - - +
634U GLU* 1.3 80.6 - - - +
636U ASN* 1.3 72.8 + - - +
637U ALA 3.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 636 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T ARG* 4.1 12.9 + - - +
23T LEU* 3.5 33.8 - - + +
632U PHE* 2.9 51.8 + - + +
633U ILE 3.5 1.3 - - - -
635U ASP* 1.3 85.0 - - - +
637U ALA* 1.3 66.1 + - - +
638U VAL* 3.2 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 637 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27T MET* 3.6 19.7 - - - -
633U ILE 2.8 16.5 + - - +
634U GLU 3.4 2.0 + - - -
635U ASP 3.5 2.8 - - - +
636U ASN* 1.3 75.1 - - - +
638U VAL* 1.3 63.3 + - - +
701U JK8 3.2 58.2 - - + -
----------------------------------------------------------
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