Contacts of the strand formed by residues 169 - 174 (chain G) in PDB entry 6V3O
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 THR 169 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ASN 4.1 2.6 + - - -
168G GLN* 1.3 75.7 + - - +
170G VAL* 1.3 73.4 + - - +
171G ASP* 4.8 4.3 - - + +
281G SER* 3.0 25.8 + - - +
282G LEU 3.7 1.3 - - - -
284G ARG* 3.8 40.0 + - + +
666G GLY 2.7 19.7 + - - +
667G SER* 3.5 9.0 + - - +
668G ILE 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G GLN* 4.1 9.6 - - - +
169G THR* 1.3 77.6 - - - +
171G ASP* 1.3 62.2 + - - +
172G LEU* 3.8 25.8 - - + -
282G LEU 3.1 11.3 + - - +
283G ILE* 3.2 12.6 - - + +
284G ARG 2.8 25.3 + - - +
668G ILE* 3.7 16.8 - - + +
670G VAL* 5.3 1.8 - - + -
694G PHE* 3.8 30.3 - - + +
695G THR* 4.9 1.6 - - - +
698G THR* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G THR* 5.0 6.1 - - + -
170G VAL* 1.3 74.9 - - - +
172G LEU* 1.3 66.4 + - - +
173G VAL* 4.0 1.1 + - - +
284G ARG* 3.3 28.0 + - + +
285G PHE 3.7 0.3 - - - -
286G SER* 2.9 25.5 + - - -
452G LYS* 4.2 8.8 + - - -
668G ILE 3.1 6.9 + - - +
669G ARG* 2.9 42.0 + - + +
670G VAL 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G VAL* 3.8 24.9 - - + -
171G ASP* 1.3 74.9 - - - +
173G VAL* 1.3 60.1 + - - +
174G PHE* 4.1 3.0 + - + -
283G ILE* 4.8 6.1 - - + -
284G ARG 3.0 8.7 + - - +
285G PHE* 3.3 26.6 - - + +
286G SER 2.9 25.1 + - - +
670G VAL* 3.5 11.2 - - + +
672G VAL* 3.8 15.3 - - + -
681G PHE* 4.0 26.0 - - + -
691G LEU* 4.4 11.0 - - + -
694G PHE* 4.0 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G ASP 4.0 7.0 - - - +
172G LEU* 1.3 76.2 - - - +
174G PHE* 1.3 67.0 + - - +
175G THR* 4.8 3.4 - - + -
286G SER* 3.4 13.2 - - - +
288G TRP* 3.6 36.3 - - + +
454G ASP* 4.2 2.5 - - - +
638G PHE* 3.6 28.0 - - + -
669G ARG* 3.7 25.1 - - - +
670G VAL 2.9 14.2 + - - +
671G THR* 3.6 4.3 - - - +
672G VAL* 2.7 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G LEU* 4.8 1.6 - - + -
173G VAL* 1.3 74.0 - - - +
175G THR* 1.3 61.6 + - - +
244G GLY* 5.4 7.2 - - - +
245G MET* 5.1 6.5 - - + -
247G TYR* 5.7 4.3 - - + -
248G ILE* 4.0 30.1 - - + -
252G VAL* 5.0 5.4 - - + -
285G PHE* 3.5 39.0 - + + -
286G SER 2.9 20.2 + - - +
287G SER* 4.7 2.9 - - - +
288G TRP* 3.1 26.2 + - - +
289G MET* 3.6 18.1 - - + +
451G VAL* 4.9 2.2 - - + -
672G VAL* 3.9 15.9 - - + -
677G ILE* 3.8 34.5 - - + -
681G PHE* 4.1 20.9 - + - -
----------------------------------------------------------
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