Contacts of the strand formed by residues 672 - 676 (chain C) in PDB entry 4P3N
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 672 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614C PHE* 4.0 19.7 - + - -
620C GLN 3.0 10.0 + - - +
621C VAL* 3.3 13.6 - - + -
622C MET* 2.9 24.4 + - - +
670C TYR* 4.1 2.1 - - - +
671C ASN* 1.3 89.2 - - + +
673C ILE* 1.3 66.0 + - - +
674C LEU* 4.2 9.2 - - + -
688C ILE* 3.8 22.2 - - + -
689C ARG 3.9 1.1 - - - -
690C THR* 4.5 8.5 - - - -
696C HIS* 5.0 0.4 - + - -
708C LEU* 3.9 26.0 - - + -
711C LEU* 4.4 0.7 - - + -
719C ALA* 3.9 27.4 - - + -
720C GLU* 3.8 25.8 - - + -
723C PHE* 3.8 26.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 673 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C MET* 3.3 12.8 - - + +
624C VAL* 4.5 15.3 - - + -
662C ILE* 3.5 40.2 - - + +
665C ALA* 3.6 21.1 - - + -
666C GLN* 3.7 19.3 - - + +
670C TYR* 4.6 7.4 - - + +
672C PHE* 1.3 79.3 - - - +
674C LEU* 1.3 63.3 + - - +
675C VAL* 3.7 19.5 + - + -
687C ASN 3.5 2.4 - - - +
688C ILE* 3.7 1.7 - - - -
689C ARG* 2.8 45.7 + - + +
690C THR 4.1 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 674 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C VAL* 3.9 25.4 - - + -
622C MET 2.9 9.3 + - - +
623C VAL* 3.5 12.4 - - + +
624C VAL 2.9 27.0 + - - +
637C VAL* 4.2 9.0 - - + -
641C PHE* 3.5 39.9 - - + -
672C PHE* 4.7 7.4 - - + -
673C ILE* 1.3 81.2 - - - +
675C VAL* 1.3 63.0 + - - +
676C VAL* 4.9 0.7 - - - -
686C VAL* 4.1 20.6 - - + -
687C ASN 3.7 2.9 - - - -
688C ILE* 4.0 30.3 - - + -
704C THR* 4.9 3.6 - - - +
708C LEU* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 675 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C VAL* 3.3 7.2 - - + +
626C VAL* 4.0 14.8 - - + -
658C LEU* 3.8 27.6 - - + -
662C ILE* 4.0 25.8 - - + -
673C ILE* 4.1 15.3 - - + +
674C LEU* 1.3 74.9 - - - +
676C VAL* 1.3 63.6 + - - +
680C GLU* 3.7 5.9 - - - +
687C ASN* 2.9 49.1 + - + +
689C ARG* 4.8 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 676 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C VAL* 4.6 7.6 - - + -
624C VAL 2.9 11.6 + - - +
625C PRO* 4.2 3.8 - - + -
626C VAL* 2.5 37.9 + - - +
630C CYS* 3.8 25.4 - - + +
633C TYR* 3.3 42.4 - - + -
634C ALA* 4.3 6.5 - - + +
637C VAL* 4.5 5.4 - - + -
674C LEU 4.6 4.9 - - - +
675C VAL* 1.3 81.0 - - - +
677C GLY* 1.3 59.9 + - - +
680C GLU* 3.8 2.7 - - + -
685C THR 4.3 1.8 - - - +
686C VAL* 4.1 18.2 - - + -
----------------------------------------------------------
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