Contacts of the strand formed by residues 680 - 687 (chain A) in PDB entry 5ES4
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 SER 680 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ASP* 6.4 1.8 - - - -
660A LEU 3.2 13.2 - - - -
661A ALA* 4.7 3.8 - - - -
673A PHE* 3.6 3.6 - - - -
676A THR* 3.3 21.5 - - - +
678A ASN* 3.1 18.4 + - - +
679A ARG* 1.3 88.3 - - - +
681A LEU* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A LEU* 3.9 1.7 - - + +
659A ASP* 3.4 3.2 - - - -
660A LEU* 2.7 47.5 + - + +
673A PHE* 3.7 33.5 - - + -
675A GLU* 3.7 34.1 - - + -
676A THR* 4.5 9.2 - - + -
680A SER* 1.3 76.0 - - - +
682A SER* 1.3 72.7 + - - +
683A ARG* 4.5 11.0 - - + +
696A PHE* 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A THR* 4.1 11.6 - - - +
658A LEU 2.7 17.2 + - - -
659A ASP* 2.9 19.5 + - - -
681A LEU* 1.3 76.9 - - - +
683A ARG* 1.3 71.6 + - - +
684A VAL* 5.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A THR* 3.8 1.0 - - - -
658A LEU* 2.9 42.7 + - + +
675A GLU* 2.9 44.0 + - - +
681A LEU* 4.5 15.4 - - + +
682A SER* 1.3 84.4 + - - +
684A VAL* 1.3 66.1 + - - +
685A ARG* 3.1 44.7 - - + +
694A GLU* 4.0 9.2 + - - +
696A PHE* 4.9 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A SER* 4.7 16.4 - - - +
656A VAL 3.5 8.3 - - - +
657A THR* 3.5 25.4 - - + +
682A SER* 5.9 0.2 - - - +
683A ARG* 1.3 76.9 - - - +
685A ARG* 1.3 79.9 + - - +
686A VAL* 6.4 0.2 - - + -
720A VAL* 5.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A SER* 3.6 3.5 - - - -
656A VAL* 3.1 40.5 + - + +
658A LEU* 4.2 21.3 - - + -
683A ARG* 3.1 46.8 + - + +
684A VAL* 1.3 89.8 + - - +
686A VAL* 1.3 65.6 + - - +
692A HIS* 3.4 35.1 + - + +
694A GLU* 2.6 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A GLN* 4.6 22.9 - - + +
654A SER 4.2 2.9 - - - +
655A SER* 4.1 16.2 - - - +
684A VAL* 6.4 0.4 - - + -
685A ARG* 1.3 79.2 - - - +
687A LEU* 1.3 74.6 + - - +
688A GLY 4.2 0.5 + - - -
692A HIS* 3.8 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A VAL* 4.6 16.4 - - + -
637A LEU* 3.0 49.6 - - + +
638A TYR* 4.0 16.2 - - - +
639A ILE* 4.3 14.1 - - + -
652A LEU 3.4 1.9 - - - +
653A GLN* 3.4 8.7 - - - -
654A SER* 3.3 35.3 + - - +
656A VAL* 3.9 25.6 - - + -
685A ARG 5.6 0.2 - - - -
686A VAL* 1.3 79.3 - - - +
688A GLY* 1.3 62.7 + - - +
691A ALA 5.0 0.7 - - - -
692A HIS* 4.0 16.2 - - + +
717A PHE* 6.4 0.2 - - + -
719A LEU* 6.1 2.7 - - + -
----------------------------------------------------------
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