Contacts of the strand formed by residues 629 - 639 (chain B) in PDB entry 1QAS
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 GLU 629 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B ARG* 3.1 27.6 - - - +
628B PRO* 1.3 74.8 - - - +
630B ARG* 1.3 62.1 + - - +
631B LEU 4.0 0.4 - - - -
691B GLU* 2.8 19.1 - - - +
692B VAL* 3.0 18.0 + - - +
695B PRO* 3.5 18.9 - - + +
723B TRP* 3.6 27.4 - - + -
754B ILE* 3.4 16.0 - - + +
755B GLN 3.4 8.4 - - - +
756B ASP* 3.1 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B GLU* 1.3 73.3 - - - +
631B LEU* 1.3 58.9 + - - +
632B ARG* 3.6 25.5 + - - +
689B GLU* 3.3 44.8 + - + +
690B PHE 3.5 4.4 + - - +
691B GLU* 3.2 33.7 + - - +
753B SER 3.4 3.3 - - - +
754B ILE* 3.5 1.2 - - - -
755B GLN* 2.9 41.3 + - + +
756B ASP* 5.2 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B GLU 4.0 0.8 + - - -
630B ARG* 1.3 73.0 - - - +
632B ARG* 1.3 62.6 - - - +
633B VAL* 3.8 21.5 - - + -
660B ILE* 3.9 22.2 - - + -
688B PHE 3.8 0.2 - - - +
689B GLU* 3.2 4.9 - - - +
690B PHE* 2.9 47.3 + - + +
700B VAL* 4.0 10.3 - - + -
723B TRP* 3.6 31.4 - - + -
726B LEU* 3.8 11.2 - - + -
752B ILE* 3.7 26.0 - - + -
753B SER 3.2 13.9 - - - +
754B ILE* 3.9 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B ARG* 3.6 23.4 + - - +
631B LEU* 1.3 76.5 - - - +
633B VAL* 1.3 62.3 + - - +
634B ARG* 4.2 0.4 - - - -
687B GLU* 3.3 34.2 + - - +
688B PHE 3.2 4.3 - - - +
689B GLU* 2.7 31.1 + - + +
751B LYS 3.6 1.2 - - - +
752B ILE* 3.5 3.1 - - - -
753B SER* 2.8 47.8 + - - +
755B GLN* 3.3 36.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B LEU* 3.8 30.1 - - + -
632B ARG* 1.3 76.9 - - - +
634B ARG* 1.3 62.4 + - - +
635B ILE* 3.8 16.6 - - + -
658B VAL* 4.6 15.3 - - + -
686B MET 3.6 2.6 - - - +
687B GLU* 3.1 3.1 - - - -
688B PHE* 2.7 46.5 + - + +
690B PHE* 4.6 3.6 - - + -
700B VAL* 5.1 1.3 - - + -
702B PHE* 3.7 31.4 - - + -
726B LEU* 5.7 0.7 - - + -
750B VAL* 4.6 2.2 - - + -
751B LYS 3.5 6.5 - - - +
752B ILE* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B ARG 6.0 0.2 - - - -
633B VAL* 1.3 71.4 - - - +
635B ILE* 1.3 61.5 + - - +
636B ILE* 3.1 18.7 + - + +
685B ASP* 2.8 57.3 + - - +
686B MET 3.4 4.9 - - - -
687B GLU* 3.5 39.4 - - + +
750B VAL* 3.2 5.7 - - - +
751B LYS* 2.9 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B VAL* 3.8 10.5 - - + -
634B ARG* 1.3 67.9 - - - +
636B ILE* 1.3 58.7 + - - +
637B SER 5.0 1.6 - - - +
656B VAL* 4.0 23.1 - - + -
658B VAL* 3.8 22.0 - - + -
672B THR* 4.2 9.4 - - + -
684B TRP* 3.5 28.3 - - + +
685B ASP 2.8 19.9 + - - -
686B MET 2.8 18.4 + - - +
688B PHE* 3.5 27.1 - - + -
702B PHE* 4.1 7.6 - - + -
748B LEU* 4.9 4.3 - - + -
749B PHE 4.9 1.6 - - - +
750B VAL* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU* 3.8 32.8 - - + -
634B ARG* 3.1 23.9 + - + +
635B ILE* 1.3 70.3 - - - +
637B SER* 1.3 58.5 + - - +
683B ARG* 3.4 7.0 - - + +
684B TRP* 2.7 30.8 + - - -
685B ASP* 2.9 28.8 + - - +
730B TYR* 4.1 15.3 - - + -
749B PHE* 3.2 33.8 + - + +
750B VAL 3.9 18.4 - - - -
751B LYS* 4.0 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLU* 2.7 33.1 + - - -
635B ILE* 5.0 0.9 - - - +
636B ILE* 1.3 80.8 - - - +
638B GLY* 1.3 57.4 + - - +
639B GLN* 2.8 15.5 + - - -
681B ASN 5.2 1.8 - - - -
682B PRO 3.2 14.4 - - - -
683B ARG* 4.0 9.0 - - - +
684B TRP* 3.7 8.7 - - - -
748B LEU* 3.5 4.2 - - - +
749B PHE* 2.7 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B SER* 1.3 75.2 - - - +
639B GLN* 1.3 67.4 + - - +
641B LEU* 4.5 2.2 - - - -
681B ASN* 3.5 5.7 - - - -
682B PRO* 2.8 35.3 + - - +
684B TRP* 3.4 14.4 - - - -
747B THR 3.5 10.1 - - - -
748B LEU* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 3.6 41.7 - - - +
280B LEU* 5.3 2.0 - - + -
637B SER* 2.8 29.5 + - - -
638B GLY* 1.3 80.7 + - - +
640B GLN* 1.3 76.3 + - + +
641B LEU* 3.3 5.0 + - - +
679B GLY 4.3 0.2 - - - -
680B PHE 3.4 8.1 - - - +
681B ASN* 5.4 0.4 - - - -
732B HIS* 3.6 2.5 - - - -
745B SER 3.4 2.9 - - - +
746B ALA* 3.6 0.2 - - - -
747B THR* 2.9 65.0 + - - +
748B LEU 3.4 0.7 + - - -
749B PHE* 3.1 17.9 + - - +
----------------------------------------------------------
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