Contacts of the strand formed by residues 124 - 127 (chain A) in PDB entry 2QCT
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 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.6 3.4 - - - +
123A LEU* 1.3 91.5 - - + +
125A ILE* 1.3 65.7 + - - +
126A VAL* 4.3 4.0 - - + -
186A TYR* 3.6 12.8 - - + +
188A PHE* 3.9 17.7 - - + -
212A VAL* 3.7 20.9 - - + +
215A TYR* 3.7 15.3 - - + -
216A GLN* 3.2 46.9 + - + +
222A PRO 4.7 0.4 + - - -
223A ILE* 3.5 23.6 - - + +
224A CYS 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.3 9.6 - - + -
114A TRP* 4.4 12.3 - - + -
117A ILE* 3.9 36.6 - - + -
122A VAL* 4.5 1.8 - - + -
124A ILE* 1.3 77.2 - - - +
126A VAL* 1.3 61.2 + - - +
127A MET 3.8 0.3 + - - -
142A TYR* 3.1 36.8 - - + +
174A LEU* 5.3 2.5 - - + -
185A ILE* 3.5 23.8 - - + -
186A TYR 3.0 11.9 + - - +
187A GLN* 3.9 8.9 - - + +
188A PHE 2.7 32.8 + - - +
224A CYS* 3.4 8.3 - - + +
226A HIS* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.3 8.5 - - + -
125A ILE* 1.3 74.3 - - - +
127A MET* 1.3 63.4 + - - +
128A ALA* 5.2 0.7 - - + -
188A PHE* 3.5 15.3 - - + +
190A TYR* 5.5 0.7 - - + -
208A LEU* 4.2 20.4 - - + -
212A VAL* 3.6 31.4 - - + -
223A ILE* 4.3 9.0 - - + -
224A CYS 2.9 9.5 + - - -
225A ILE* 3.4 22.7 - - + +
226A HIS* 3.0 26.2 + - - +
237A ILE* 4.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.8 2.0 + - + -
126A VAL* 1.3 72.5 - - - +
128A ALA* 1.3 56.6 + - - +
129A CYS* 3.5 15.3 + - + +
131A GLU 4.8 3.1 - - - +
139A CYS* 3.5 31.2 - - + -
142A TYR* 3.4 10.3 - - - +
143A TRP* 3.4 41.3 - - + -
187A GLN* 3.7 12.3 - - - +
188A PHE 3.1 6.7 + - - +
189A HIS* 3.4 32.7 - - + +
190A TYR* 2.8 32.2 + - - +
226A HIS* 3.2 27.4 - - + +
----------------------------------------------------------
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