Contacts of the strand formed by residues 681 - 685 (chain A) in PDB entry 6RUT
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 681 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PHE* 3.7 20.4 - + + -
544A TYR* 3.5 33.4 - + - +
576A ARG* 3.6 48.4 + - + +
578A LEU* 4.2 19.3 - - + -
657A VAL* 3.5 35.4 - - + -
658A ARG 3.5 2.7 - - - -
659A LEU* 4.3 2.7 - - + -
660A ASN* 4.4 0.2 - - - -
678A PRO 3.3 7.1 + - - +
679A ILE 3.2 0.8 - - - -
680A SER* 1.4 77.2 - - - +
682A SER* 1.4 62.3 + - - +
683A PHE* 3.8 26.7 - - + -
759A ALA* 3.5 16.9 - - - +
----------------------------------------------------------
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 VAL* 3.1 8.3 - - - +
658A ARG* 2.8 36.6 + - - -
660A ASN* 4.4 0.2 - - - -
681A PHE* 1.4 79.8 - - - +
683A PHE* 1.4 61.5 + - - +
759A ALA* 3.9 11.1 + - - +
760A PRO 3.4 23.1 + - - -
761A SER* 3.1 28.5 - - - -
762A ALA 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A LEU* 3.8 27.1 - - + -
579A PRO 5.9 1.3 - - - -
581A PRO* 5.7 2.0 - - + -
652A THR* 3.3 25.1 - - - -
653A ARG 4.7 4.3 - - - -
654A GLY* 3.7 7.9 - - - -
655A GLY* 3.5 29.4 - - - -
656A VAL 3.4 12.6 - - - -
657A VAL* 4.5 5.2 - - + -
681A PHE* 3.8 16.7 - - + -
682A SER* 1.4 76.4 + - - +
684A THR* 1.3 65.9 + - - +
685A PRO* 3.8 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 684 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A VAL* 3.0 37.2 + - + +
683A PHE* 1.3 78.9 + - - +
685A PRO* 1.3 81.5 - - + +
686A PHE* 4.7 0.3 - - - -
761A SER* 3.8 17.3 + - - -
762A ALA 3.3 27.8 + - - +
763A LEU* 4.7 15.5 - - + -
764A ALA 5.6 0.2 - - - +
513B ILE* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 685 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A GLY 3.5 10.1 - - - +
656A VAL* 5.6 0.3 - - - +
683A PHE* 3.8 20.4 - - + +
684A THR* 1.3 100.1 - - + +
686A PHE* 1.3 68.2 + - - +
687A THR* 5.3 2.1 - - - +
763A LEU* 5.7 2.6 - - - +
764A ALA 5.5 3.5 + - - +
513B ILE* 3.8 36.6 - - + -
----------------------------------------------------------
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