Contacts of the strand formed by residues 80 - 84 (chain C) in PDB entry 3GXM
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 GLY 80 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL* 3.7 5.5 - - - +
79C LYS* 1.3 83.7 - - - +
81C PHE* 1.3 70.6 + - - -
117C ASN* 3.2 12.3 - - - -
118C ILE* 3.5 9.2 - - - +
376C VAL 3.5 2.8 + - - -
377C GLY* 3.2 4.4 - - - -
378C TRP* 2.8 30.3 + - - -
427C ILE 5.2 2.2 - - - -
429C GLU* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL* 4.2 5.4 - - + -
80C GLY* 1.3 79.9 - - - -
82C GLY* 1.3 58.8 + - - +
115C GLY 5.8 0.2 - - - +
116C TYR* 3.5 6.8 - - + -
117C ASN* 2.8 33.7 + - - +
118C ILE* 3.2 4.7 + - - +
367C ILE* 4.1 10.8 - - + -
371C LEU* 5.4 2.5 - - + -
378C TRP* 3.4 50.5 - + + -
420C LEU* 4.9 11.7 - - + -
423C PHE* 3.7 28.9 - - + -
424C SER* 3.4 34.5 - - - -
427C ILE* 3.8 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 1.3 75.7 - - - +
83C GLY* 1.3 53.1 + - - -
116C TYR* 3.4 25.1 - - - -
118C ILE* 3.0 17.3 - - - -
378C TRP* 2.9 10.0 + - - +
379C THR* 3.5 4.2 - - - -
380C ASP* 2.8 33.0 + - - +
420C LEU* 5.2 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLY* 1.3 75.0 - - - -
84C ALA* 1.3 63.4 + - - -
116C TYR* 3.7 4.9 - - - -
118C ILE 3.3 4.2 + - - -
119C ILE* 3.3 11.3 - - - +
120C ARG 3.0 16.8 + - - -
379C THR* 3.8 6.6 + - - -
380C ASP* 3.3 17.0 - - - -
381C TRP 3.9 2.5 - - - -
383C LEU* 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLY* 1.3 71.2 - - - -
85C MET* 1.3 61.0 + - - +
86C THR* 3.1 9.1 + - + -
89C ALA* 3.9 0.9 - - - +
120C ARG* 3.2 24.2 - - + +
122C PRO* 4.9 1.3 - - + -
380C ASP 3.2 3.3 + - - +
381C TRP* 3.0 50.9 + - + +
382C ASN* 3.7 2.6 - - - -
383C LEU* 3.1 27.7 + - - +
----------------------------------------------------------
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