Contacts of the strand formed by residues 626 - 633 (chain B) in PDB entry 1M7X
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 PHE 626 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ILE* 3.3 28.6 - - + +
515B TYR* 3.8 15.7 + - - +
560B PHE* 4.6 4.9 - + - -
561B PRO* 3.6 31.6 - - + -
623B PRO 3.0 17.2 + - - +
624B TYR 3.2 2.9 + - - -
625B GLY* 1.3 81.1 - - - +
627B GLU* 1.3 64.6 + - - +
628B TRP* 3.8 48.9 - + - -
641B PHE* 3.3 47.6 - + + -
642B VAL 3.4 4.5 - - - -
643B ARG* 3.8 11.0 - - - -
644B ARG* 4.5 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B PHE* 1.3 79.9 - - - +
628B TRP* 1.3 71.8 + - - +
629B LEU* 3.5 1.5 + - + +
641B PHE* 3.2 3.7 - - - -
642B VAL* 2.7 51.1 + - + +
644B ARG* 2.6 39.6 + - - +
670B ASN* 3.3 15.4 + - - +
707B ARG* 4.0 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU 4.1 1.6 - - - -
508B THR* 3.6 40.0 + - + -
511B ILE* 3.7 27.4 - - + +
512B LEU* 5.8 3.0 - - - +
556B TRP* 3.8 30.3 - + - -
560B PHE* 5.3 0.7 - + - -
626B PHE* 3.8 18.4 - + - -
627B GLU* 1.3 75.8 - - - +
629B LEU* 1.3 59.4 + - - +
630B VAL 3.9 8.3 - - - -
631B VAL* 3.5 39.7 - - + +
639B LEU* 4.2 9.6 - - + -
640B ILE 3.7 13.2 - - - -
641B PHE* 3.9 14.1 - + + -
707B ARG* 3.3 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B GLU* 3.5 3.8 + - + +
628B TRP* 1.3 81.1 - - - +
630B VAL* 1.3 65.1 + - - +
631B VAL 4.2 0.4 - - - -
640B ILE* 2.6 37.0 + - + +
641B PHE 4.1 13.7 - - - +
642B VAL* 4.4 6.3 - - + +
650B GLU* 5.8 0.7 - - - +
652B ILE* 4.2 19.7 - - + -
667B PHE* 3.9 12.8 - - + -
668B GLY 3.7 25.0 - - - +
669B ILE* 4.4 6.1 - - + -
670B ASN* 3.9 20.9 - - - +
705B HIS* 3.9 17.3 + - - +
707B ARG* 3.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B TRP* 3.9 2.9 - - - -
629B LEU* 1.3 83.8 - - - +
631B VAL* 1.3 57.9 + - - +
632B ASP* 4.5 3.1 - - - +
633B ASP* 3.8 22.4 - - + +
638B VAL 3.9 6.0 - - - +
639B LEU* 3.6 6.6 - - - -
640B ILE* 2.8 44.0 + - + +
665B TYR* 3.6 21.3 - - - +
667B PHE* 3.4 31.4 - - + -
705B HIS* 3.7 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B HIS* 3.1 22.8 + - - -
508B THR* 3.9 16.9 - - + +
628B TRP* 3.5 51.8 - - + +
629B LEU 4.2 0.4 - - - -
630B VAL* 1.3 74.9 - - - +
632B ASP* 1.3 71.5 + - + +
633B ASP 3.8 1.3 - - - -
634B LYS* 5.6 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B HIS* 4.2 2.2 - - - -
630B VAL* 4.6 5.7 - - - +
631B VAL* 1.3 91.6 + - + +
633B ASP* 1.3 62.6 + - - +
634B LYS* 2.9 23.9 + - + +
705B HIS* 5.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B HIS* 3.3 9.2 + - - -
630B VAL* 3.8 8.9 - - + +
631B VAL 3.8 2.0 - - - -
632B ASP* 1.3 76.9 + - - +
634B LYS* 1.3 54.6 + - - +
635B GLU* 3.8 6.3 + - - +
636B ARG* 3.1 54.8 + - - +
637B SER 3.1 17.2 + - - -
638B VAL* 3.2 22.3 + - - +
665B TYR* 2.6 30.6 + - - +
----------------------------------------------------------
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