Contacts of the strand formed by residues 150 - 154 (chain B) in PDB entry 1GQC
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 150 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.9 11.9 - - + -
143B VAL 3.6 4.9 - - - -
148B GLN 3.7 1.4 + - - -
149B ASP* 1.3 77.9 - - - +
151B LEU* 1.3 62.1 + - - +
152B TYR 4.6 0.2 - - - +
153B PHE* 3.5 38.1 - - + -
206B MET* 3.2 16.8 - - + +
211B ASN* 4.7 3.3 - - - +
212B ILE 2.9 21.3 + - - +
214B THR* 4.1 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 2.8 39.8 - - - +
152A TYR* 4.0 20.6 - - + -
194A PRO* 5.4 4.0 - - + -
203A LEU* 5.7 0.7 - - + -
206A MET* 4.3 38.8 - - + +
207A ASN* 5.1 1.6 - - - +
143B VAL* 2.7 40.3 + - + +
144B VAL 4.4 9.2 - - - +
145B ASN* 4.4 17.0 - - + +
149B ASP 4.4 3.6 - - - +
150B ALA* 1.3 78.5 - - - +
152B TYR* 1.3 60.7 + - - +
206B MET* 3.9 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 3.7 28.2 - - + +
151A LEU* 4.3 11.4 - - + -
152A TYR* 3.5 24.7 - - + -
158A ILE* 4.1 17.7 - - + -
159A PRO* 3.3 20.6 - - - +
141B LYS 3.8 0.3 - - - +
142B VAL* 3.5 6.6 - - - +
143B VAL* 3.3 23.2 + - + +
150B ALA 3.6 1.0 - - - -
151B LEU* 1.3 84.9 - - - +
153B PHE* 1.3 73.5 + - - +
154B SER* 3.5 22.0 - - - -
158B ILE* 3.9 12.6 - - + +
194B PRO* 4.2 4.5 - - + +
198B GLU* 2.7 35.0 + - - +
203B LEU* 4.0 19.1 - - + +
206B MET* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 4.2 7.2 - - + -
140B VAL* 4.3 1.6 - - + -
141B LYS 3.3 5.4 - - - +
142B VAL* 3.8 19.5 - - + -
150B ALA* 3.5 30.5 - - + -
152B TYR* 1.3 84.5 - - - +
154B SER* 1.3 61.2 + - - +
172B HIS* 3.4 49.1 - + + -
176B TYR* 5.9 0.2 - + - -
198B GLU* 3.8 1.0 - - - +
200B LEU* 3.3 16.4 - - + +
202B GLN* 3.5 26.7 - - + +
203B LEU* 3.6 18.0 - - + +
206B MET* 3.7 19.7 - - - -
212B ILE* 4.0 30.3 - - + -
214B THR* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 3.7 5.0 - - - +
140B VAL* 3.7 4.2 - - - +
141B LYS* 2.7 42.2 + - - +
152B TYR* 3.5 13.0 - - - -
153B PHE* 1.3 74.3 - - - +
155B ARG* 1.3 60.9 + - - +
156B SER* 3.0 26.6 + - - -
158B ILE* 3.6 19.9 - - - +
198B GLU* 2.7 23.3 + - - -
200B LEU* 4.0 0.9 - - - +
----------------------------------------------------------
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