Contacts of the strand formed by residues 620 - 628 (chain L) in PDB entry 2O93
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 GLN 620 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612L THR* 3.3 21.6 - - - +
613L GLU 3.3 5.4 - - - +
614L LYS* 3.5 26.1 + - - +
618L GLY 3.0 6.2 + - - +
619L GLN* 1.3 69.3 - - - +
621L ILE* 1.3 56.9 - - - +
622L TRP 3.0 23.0 + - - +
623L GLU* 3.1 47.1 + - - +
659L TYR* 5.3 1.9 - - - -
667L ARG* 5.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 621 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613L GLU* 2.5 37.9 + - + +
614L LYS* 4.6 1.6 - - - +
615L THR* 3.5 26.5 - - + -
619L GLN* 2.8 23.3 + - + +
620L GLN* 1.3 71.2 - - - +
622L TRP* 1.3 59.0 + - - +
646L ARG* 3.4 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 622 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611L PHE* 4.1 17.3 - - + -
612L THR* 3.5 29.1 - - - -
613L GLU* 3.5 11.9 + - + -
620L GLN* 3.0 25.7 + - - +
621L ILE* 1.3 79.2 - - - +
623L GLU* 1.3 70.2 + - - +
624L MET* 3.5 40.6 - - + +
643L PRO* 4.8 1.1 - - + -
644L GLU 3.7 16.2 - - - -
645L TYR* 3.8 25.6 - + - -
646L ARG* 3.5 43.7 - - + +
656L VAL* 4.2 6.5 - - + -
675L TYR* 3.8 28.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 623 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610L VAL* 3.8 22.4 - - + -
611L PHE 3.2 6.7 - - - +
620L GLN* 3.1 24.0 + - - +
622L TRP* 1.3 88.1 - - - +
624L MET* 1.3 60.5 - - - +
625L GLU 4.3 0.9 + - - -
659L TYR* 4.8 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 624 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610L VAL* 3.6 3.4 - - - -
611L PHE* 2.7 39.3 + - + +
622L TRP* 3.5 39.4 - - + +
623L GLU* 1.3 77.8 - - - +
625L GLU* 1.3 68.3 + - - +
626L ALA 3.8 0.2 + - - -
643L PRO* 3.5 29.4 - - + -
644L GLU 4.8 5.4 - - - +
646L ARG* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 625 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608L LYS* 3.3 37.0 + - - +
609L VAL 3.5 15.9 - - - +
610L VAL* 4.3 12.7 - - + +
623L GLU 4.3 0.4 + - - -
624L MET* 1.3 88.4 - - - +
626L ALA* 1.3 72.5 + - - +
627L THR* 4.1 0.7 + - - -
643L PRO* 4.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 626 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608L LYS* 5.5 0.3 - - - -
609L VAL* 2.8 21.9 + - + +
611L PHE* 3.9 9.0 - - + -
624L MET 3.8 1.8 + - - -
625L GLU* 1.3 87.9 - - - +
627L THR* 1.3 63.5 + - - +
628L VAL* 3.7 3.5 + - - +
640L VAL* 3.3 26.9 - - + -
641L GLU 3.3 12.6 - - - +
643L PRO* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 627 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625L GLU 4.1 1.3 + - - -
626L ALA* 1.3 72.4 - - - +
628L VAL* 1.3 74.4 + - - +
629L ASP* 4.2 0.4 + - - -
640L VAL* 3.4 2.1 - - - +
641L GLU* 2.6 65.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 628 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605L SER 5.1 2.5 - - - +
607L SER 4.1 19.3 - - - +
608L LYS* 4.5 0.9 - - - -
609L VAL* 3.6 35.2 - - + +
626L ALA 3.7 2.8 + - - +
627L THR* 1.3 86.5 - - - +
629L ASP* 1.3 66.3 + - - +
630L LYS* 3.0 27.5 + - + +
633L SER* 3.5 17.9 - - - +
638L LEU* 3.8 13.0 - - + -
639L PHE 3.4 13.7 - - - +
640L VAL* 4.1 1.8 - - + -
----------------------------------------------------------
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