Contacts of the strand formed by residues 110 - 115 (chain D) in PDB entry 6QPA
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 110 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 5.0 6.3 - - + -
14D LYS 3.8 3.1 - - - +
15D ILE* 4.4 11.7 - - + +
106D CYS* 3.4 22.4 - - + +
107D LEU* 3.1 33.1 + - + +
108D GLY 3.6 0.7 - - - -
109D MET* 1.3 78.8 - - + +
111D ILE* 1.3 66.1 + - - +
112D GLU 3.4 23.8 - - - +
113D GLY 3.6 19.3 - - - +
114D PRO* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS 2.7 14.9 + - - +
16D ALA* 3.8 28.5 - - + +
72D ASN* 4.1 11.0 - - - +
73D PRO* 3.6 41.1 - - + -
109D MET 3.7 1.1 + - - +
110D VAL* 1.3 78.6 - - - +
112D GLU* 1.3 60.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 3.5 1.8 - - - -
14D LYS* 2.9 66.0 + - + +
73D PRO* 5.6 1.0 - - - +
110D VAL* 3.4 8.3 - - - +
111D ILE* 1.3 80.0 - - + +
113D GLY* 1.3 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D MET 3.9 5.8 - - - -
107D LEU* 5.4 1.0 - - - +
110D VAL* 3.6 11.7 - - - +
112D GLU* 1.3 84.0 - - - +
114D PRO* 1.3 76.7 - - - +
115D TRP* 3.9 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.4 31.6 - - - +
12D MET 3.3 5.8 - - - +
13D ALA* 4.5 4.5 - - + -
107D LEU* 4.8 17.0 - - + -
110D VAL* 4.9 4.0 - - + -
113D GLY* 1.3 84.7 - - - +
115D TRP* 1.3 61.0 + - - +
208D GLY 4.0 13.5 - - - +
209D SER* 3.2 24.7 - - - +
210D PHE* 4.3 21.8 - - + -
211D GLN* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 4.5 0.4 - - - -
12D MET* 2.8 44.3 + - + +
113D GLY* 5.0 3.1 - - - -
114D PRO* 1.3 75.4 - - - +
116D GLU* 1.3 57.3 + - - +
117D PRO* 3.3 35.3 - - + +
201D GLN* 5.3 3.2 + - - +
204D VAL* 3.6 31.7 - - + +
209D SER* 3.5 30.7 - - - -
211D GLN* 4.1 22.4 - - + -
245D ILE* 4.0 19.5 - - + -
----------------------------------------------------------
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