Contacts of the helix formed by residues 174 - 180 (chain G) in PDB entry 5TWV
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 ALA 174 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU 5.8 1.8 + - - -
172G ALA 3.3 3.8 + - - +
173G GLN* 1.3 70.6 - - - +
175G HIS* 1.3 65.8 + - - +
176G ARG 3.3 1.8 - - - +
177G ARG* 3.6 22.2 + - + +
178G ALA 3.6 2.6 + - - -
291G VAL* 5.4 2.9 - - + -
294G THR* 4.5 10.3 - - - +
296G ILE* 4.1 32.8 - - + +
298G THR* 3.4 28.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 175 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 3.8 50.5 + - + +
293A THR* 5.3 5.5 - - - +
173G GLN* 3.5 30.9 - - + +
174G ALA* 1.3 78.3 - - - +
176G ARG* 1.3 72.7 + - + +
178G ALA* 3.0 22.4 + - - +
179G GLU* 3.1 10.6 + - - +
298G THR* 4.3 8.8 + - - -
299G GLN 5.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ARG* 5.7 5.5 - - - +
57E GLN* 5.7 14.3 - - + +
58E ASP* 4.0 30.7 - - + +
173G GLN* 4.9 28.9 + - + +
174G ALA 3.3 0.4 - - - -
175G HIS* 1.3 88.3 - - + +
177G ARG* 1.3 62.5 + - + +
179G GLU* 3.2 21.7 + - - +
180G THR* 4.1 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E ASP* 5.9 1.8 - - - -
61E THR* 3.9 39.5 + - - +
174G ALA* 3.6 20.7 + - + +
175G HIS 3.2 0.6 - - - -
176G ARG* 1.3 79.3 - - + +
178G ALA* 1.3 55.9 + - - +
180G THR* 2.5 38.8 + - - +
181G LEU* 4.3 3.7 - - - +
204G ASP* 4.7 3.4 + - - -
206G ARG* 3.9 24.5 - - - +
208G SER* 3.5 42.9 + - - -
209G MET 4.6 9.4 + - - -
210G ILE* 5.4 6.4 - - - +
291G VAL* 4.9 20.2 - - + +
292G GLU* 5.4 1.0 - - - +
293G THR* 4.8 9.1 + - - +
294G THR* 5.8 1.1 - - - +
298G THR* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G ALA 3.6 1.8 + - - -
175G HIS* 3.0 11.9 + - - +
177G ARG* 1.3 79.5 - - - +
179G GLU* 1.3 62.1 + - - +
181G LEU* 3.0 37.2 - - + +
298G THR* 3.0 35.8 - - + +
299G GLN 4.2 13.2 - - - +
300G ALA* 4.3 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ARG* 5.0 26.5 + - + +
39G LYS* 3.3 40.4 + - - +
175G HIS 3.1 10.3 + - - +
176G ARG* 3.2 15.3 + - - +
178G ALA* 1.3 70.8 - - - +
180G THR* 1.3 54.2 + - + +
181G LEU 2.6 27.6 + - - +
182G ILE* 3.9 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ARG* 6.3 3.4 - - + -
55E PHE* 4.1 14.4 - - + -
176G ARG 4.3 7.9 - - - +
177G ARG* 2.5 31.0 + - - +
179G GLU* 1.3 70.2 - - + +
181G LEU* 1.3 57.6 + - - +
182G ILE* 3.4 7.8 + - - -
204G ASP* 3.7 13.1 + - - -
205G LEU* 3.3 39.7 + - + +
206G ARG* 3.5 36.4 - - + +
----------------------------------------------------------
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