Contacts of the strand formed by residues 175 - 181 (chain B) in PDB entry 1C7G
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 ILE 175 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 4.7 3.5 + - - -
116B TYR* 3.3 18.8 - - + +
118B ALA* 4.7 6.3 - - + +
163B LEU* 5.8 1.6 - - + -
166B LEU* 4.0 26.2 - - + +
167B ILE* 3.8 26.0 - - + -
170B LYS* 5.2 2.7 - - + -
171B GLY 3.9 14.8 - - - +
172B ALA* 2.9 12.7 + - - +
173B GLU 3.5 1.1 - - - -
174B ASN* 1.3 80.9 - - + +
176B ALA* 1.3 66.4 + - - +
177B TYR* 3.8 17.9 - - - +
178B ILE* 4.8 5.4 - - + +
209B ILE* 3.6 42.8 - - + +
210B LYS 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 3.4 23.0 - - - +
111B ILE* 4.1 5.8 - - + -
115B GLN* 3.6 23.4 + - + +
116B TYR 2.7 16.3 + - - +
117B VAL* 3.9 11.0 - - + -
174B ASN 3.9 2.6 + - - -
175B ILE* 1.3 73.7 - - - +
177B TYR* 1.3 75.1 - - + +
210B LYS* 3.8 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.1 20.3 - - + +
107B SER* 3.8 17.8 + - - -
110B ALA* 3.6 31.4 - - + -
111B ILE* 3.7 22.6 - - + +
117B VAL* 3.6 24.0 - - + +
118B ALA 3.6 17.5 + - - -
130B GLN* 3.9 10.0 + - - +
175B ILE* 3.3 5.0 - - - +
176B ALA* 1.3 88.6 - - + +
178B ILE* 1.3 73.0 + - - +
179B CYS* 4.1 14.3 - - + -
209B ILE* 4.2 5.2 - - - -
210B LYS* 3.0 28.5 - - + +
212B PHE* 3.5 20.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ALA* 3.2 17.3 - - + +
140B ILE* 4.7 2.0 - - + -
158B ILE* 4.2 24.7 - - + -
163B LEU* 4.1 32.3 - - + -
167B ILE* 5.9 0.2 - - + -
175B ILE* 4.8 3.1 - - + -
177B TYR* 1.3 75.6 - - - +
179B CYS* 1.3 60.4 + - - +
180B LEU* 3.5 9.6 + - + +
200B VAL* 4.5 11.4 - - + -
204B ALA* 3.8 22.7 - - + -
209B ILE* 3.7 26.0 - - + -
210B LYS 2.5 11.4 + - - +
211B ILE* 3.5 11.6 - - + +
212B PHE 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 6.5 0.7 - - - -
117B VAL* 4.3 10.3 - - + -
118B ALA 2.7 13.3 + - - +
119B GLY* 3.2 22.8 - - - -
120B ASN* 3.4 4.9 - - - +
121B MET 5.2 1.4 - - - +
126B THR* 4.8 8.5 - - - -
130B GLN* 4.1 13.7 - - - +
137B PHE* 5.9 2.2 - - + -
177B TYR* 3.9 18.5 + - + -
178B ILE* 1.3 70.8 - - - +
180B LEU* 1.3 57.4 - - - +
181B ALA* 3.6 2.6 + - - +
212B PHE* 3.3 10.5 - - - -
213B TYR 5.3 0.7 - - - -
214B ASP* 4.5 20.9 - - - -
252B THR* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASN* 3.6 6.5 - - - +
158B ILE* 3.8 27.4 - - + -
178B ILE* 3.5 4.1 + - + +
179B CYS* 1.3 70.8 - - - +
181B ALA* 1.3 63.0 + - - +
182B VAL* 3.7 27.3 + - + -
192B VAL* 4.0 18.2 - - + -
196B ASN* 4.9 1.1 - - - +
197B MET* 4.1 19.7 - - + +
200B VAL* 4.3 24.2 - - + -
211B ILE* 4.8 4.3 - - + -
212B PHE 3.3 6.1 + - - -
213B TYR* 3.1 34.6 - - + +
214B ASP* 2.9 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASN* 2.9 42.4 + - - +
121B MET 5.9 0.7 - - - +
122B TYR* 6.6 0.4 - - - -
179B CYS* 3.6 3.6 + - - +
180B LEU* 1.3 72.5 - - - +
182B VAL* 1.3 64.9 + - - +
183B THR 3.5 11.4 - - - +
184B VAL* 3.5 12.5 - - + +
185B ASN 5.8 0.2 - - - +
192B VAL* 3.6 1.4 - - - +
214B ASP* 3.8 25.1 - - + +
1000B PLP 5.2 4.5 - - + -
----------------------------------------------------------
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