Contacts of the helix formed by residues 175 - 179 (chain A) in PDB entry 2FGY
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 ASP 175 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A CYS* 3.1 24.6 - - + +
174A ALA* 1.3 77.7 - - - +
176A GLY* 1.3 66.7 + - - +
177A ARG* 2.8 64.6 + - - +
178A LEU* 3.0 15.7 + - + +
179A LYS* 3.9 2.6 + - - +
242A HIS* 3.2 20.1 + - + +
252A GLY 4.4 0.7 - - - +
253A CYS* 5.2 0.2 - - - -
254A ALA 5.5 0.7 + - - -
397A HIS* 3.1 22.2 + - + -
418A TYR* 4.1 9.0 - - - -
620A ZN 3.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ALA 3.3 2.4 + - - -
175A ASP* 1.3 70.5 + - - +
177A ARG* 1.3 53.9 + - - +
178A LEU 3.1 0.4 - - - -
179A LYS* 3.0 18.2 + - - +
399A GLU* 2.9 30.7 + - - +
415A ASN* 2.6 28.4 + - - -
417A ALA 3.2 24.2 + - - -
418A TYR* 4.2 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 2.8 43.2 + - - +
176A GLY* 1.3 75.2 - - - +
178A LEU* 1.3 65.0 + - - +
179A LYS 3.4 0.4 - - - -
180A GLY 4.9 0.2 + - - -
185A ILE* 4.4 8.1 - - - +
242A HIS* 4.0 3.8 - - - -
251A SER* 2.9 33.8 + - - +
252A GLY 3.3 11.7 + - - -
297A THR* 3.5 28.6 + - + +
300A ASP* 4.6 1.2 - - - +
395A ILE 2.9 29.7 + - - -
396A GLY* 3.4 33.8 + - - -
397A HIS* 3.9 14.1 + - - +
414A ARG* 3.4 47.1 + - + +
415A ASN* 3.9 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A PRO* 3.8 17.3 - - + +
173A CYS* 3.7 35.9 - - + +
175A ASP* 3.0 13.3 + - + +
177A ARG* 1.3 81.9 - - - +
179A LYS* 1.3 59.9 + - - +
180A GLY 3.1 3.8 - - - -
181A LEU* 2.9 30.4 + - + +
185A ILE* 4.2 7.2 - - + -
240A VAL* 4.4 11.2 - - + +
242A HIS* 3.8 33.2 - - + -
295A VAL* 4.0 37.9 - - + -
297A THR* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP 3.9 1.5 + - - +
176A GLY 3.0 19.0 + - - +
177A ARG 3.4 0.4 - - - -
178A LEU* 1.3 77.6 - - - +
180A GLY* 1.3 55.5 + - - +
181A LEU* 3.2 3.2 + - - +
196A ARG* 5.3 5.7 - - - +
403A SER* 5.8 1.2 + - - -
407A GLY* 5.1 0.6 - - - -
408A PHE 4.8 11.8 + - - +
411A VAL 4.2 7.4 - - - +
412A GLN* 3.2 39.4 + - - +
413A ILE 3.3 24.5 - - - +
415A ASN 4.5 0.2 - - - +
417A ALA* 3.6 35.2 - - + +
419A TYR* 3.3 45.3 - - + +
----------------------------------------------------------
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