Contacts of the strand formed by residues 165 - 169 (chain H) in PDB entry 1GC1
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 VAL 165 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H PRO* 4.4 2.0 - - + -
157H VAL* 4.3 8.1 - - + -
160H TYR* 3.8 15.5 - - + +
163H GLN* 2.6 11.5 + - - +
164H PRO* 1.3 71.6 - - - +
166H THR* 1.3 64.4 + - - +
167H VAL* 4.5 7.6 - - + -
180H THR* 6.2 0.2 - - + -
193H LEU* 3.7 37.5 - - + -
213H VAL* 4.1 18.2 - - + -
214H ASN 3.2 18.4 - - - +
215H HIS* 4.2 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 166 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164H PRO 5.6 1.1 - - - -
165H VAL* 1.3 79.0 - - - +
167H VAL* 1.3 65.5 + - - +
168H SER* 5.3 2.6 + - - -
212H ASN 3.5 1.1 - - - +
213H VAL* 3.4 3.5 - - - +
214H ASN* 2.9 57.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H VAL* 4.1 24.0 - - + -
165H VAL* 4.5 11.0 - - + -
166H THR* 1.3 81.2 - - - +
168H SER* 1.3 76.1 + - - +
169H TRP* 5.5 0.7 - - - -
180H THR* 4.4 23.7 + - + +
193H LEU* 5.1 2.0 - - + -
195H SER* 3.4 32.5 - - - +
211H CYS* 4.3 13.0 - - + -
212H ASN 3.1 7.6 - - - +
213H VAL* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H THR* 5.3 2.6 + - - -
167H VAL* 1.3 78.7 + - - +
169H TRP* 1.3 70.0 + - - +
171H SER* 5.0 0.7 - - - -
172H GLY* 4.3 13.7 - - - -
211H CYS* 3.0 10.6 - - - +
212H ASN* 2.8 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H LEU* 4.0 8.7 - - + -
154H GLY* 3.3 28.5 - - - -
167H VAL 5.5 0.7 - - - -
168H SER* 1.3 81.6 + - - +
170H ASN* 1.3 71.5 + - - +
171H SER 3.1 2.0 - - - -
172H GLY 2.9 11.1 + - - -
174H LEU* 3.2 39.7 + - + +
178H VAL* 3.6 31.4 - - + +
180H THR* 5.6 0.7 - - - -
195H SER* 3.1 46.3 + - - -
197H VAL* 3.9 16.3 - - + +
209H TYR* 4.3 5.6 - - + -
210H ILE 3.0 31.9 - - - -
211H CYS* 3.5 31.2 - - + -
226H VAL* 3.8 17.9 - - + -
----------------------------------------------------------
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