Contacts of the strand formed by residues 139 - 145 (chain D) in PDB entry 2V32
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 LEU 139 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 5.2 0.7 - - - +
144C LEU* 5.5 0.2 - - + -
3D ILE* 3.6 38.6 - - + +
4D THR 3.6 26.9 - - - +
5D LEU* 3.6 16.9 - - + +
6D GLY* 2.8 28.8 + - - -
7D GLU 2.9 13.3 + - - +
9D PHE* 4.3 7.3 - - + +
131D PHE* 3.7 28.0 - - + -
132D ILE 3.8 9.0 - - - +
133D ILE* 4.5 3.6 - - - +
137D LYS 3.9 1.0 + - - -
138D LYS* 1.3 72.5 - - - +
140D LYS* 1.3 59.4 + - - +
141D LEU 3.4 22.4 - - - +
142D SER* 4.2 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 5.8 4.1 - - + +
116C ASP* 5.7 2.2 + - - -
146C PRO* 3.4 26.2 - - - +
5D LEU* 3.9 8.3 - - - +
6D GLY* 5.7 2.0 - - - -
31D TRP* 4.0 18.2 - - + -
132D ILE 2.8 12.6 + - - +
134D GLY* 3.6 16.8 - - - +
136D ASP* 2.8 42.7 + - - -
138D LYS* 3.5 21.4 - - - +
139D LEU* 1.3 77.1 + - - +
141D LEU* 1.3 63.6 + - - +
163D LEU* 4.1 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU 3.4 16.2 - - - +
145C TYR* 3.6 38.1 - - + +
146C PRO* 3.9 10.8 - - + -
149C THR* 4.4 2.9 - - + -
5D LEU* 3.7 4.7 - - - +
130D VAL* 5.5 1.6 - - + +
131D PHE* 3.7 0.2 - - - -
132D ILE* 2.9 45.7 + - + +
139D LEU* 3.4 7.8 - - - +
140D LYS* 1.3 81.4 - - - +
142D SER* 1.3 72.6 + - - +
143D ILE* 4.0 7.9 - - + -
156D ILE* 6.5 0.2 - - + -
159D VAL* 3.8 30.7 - - + -
163D LEU* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 2.7 62.2 + - - +
3D ILE 5.1 1.0 + - - -
5D LEU* 4.2 1.0 - - - +
130D VAL 3.2 13.7 - - - -
131D PHE* 3.7 23.7 - - - -
139D LEU* 4.2 8.9 - - - +
141D LEU* 1.3 77.7 - - - +
143D ILE* 1.3 67.6 + - - +
144D LEU* 5.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C SER 3.6 5.6 - - - -
143C ILE* 3.8 24.7 - - + +
145C TYR* 4.2 8.5 - - + +
128D ARG 4.6 1.6 - - - +
129D ALA* 3.4 3.5 - - - +
130D VAL* 3.0 62.5 + - + +
131D PHE* 5.5 0.3 - - - -
141D LEU* 4.0 15.5 - - + -
142D SER* 1.3 80.9 - - - +
144D LEU* 1.3 65.9 + - - +
145D TYR* 3.4 30.3 - - + +
151D ARG* 3.9 15.7 - - + -
152D ASN 6.0 0.2 - - - +
156D ILE* 5.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE 4.5 10.3 - - - +
4C THR* 4.7 0.4 - - - -
5C LEU* 3.8 31.8 - - + +
141C LEU* 3.4 8.3 - - - +
142C SER* 2.9 49.5 + - - +
110D LEU 5.1 0.7 - - - +
111D GLY 3.7 26.9 - - - +
112D MET* 4.3 2.9 - - + -
127D CYS* 4.0 8.3 - - - -
128D ARG 4.2 2.0 - - - -
129D ALA* 4.0 18.8 - - + +
131D PHE* 4.9 9.6 - - + -
142D SER* 5.9 2.0 - - - +
143D ILE* 1.3 79.0 - - - +
145D TYR* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 3.8 2.7 - - - -
141C LEU* 3.7 23.8 - - + -
143C ILE* 4.3 7.3 - - + +
155C GLU* 2.6 34.7 + - - +
159C VAL* 3.6 23.8 - - + +
127D CYS* 3.3 5.2 - - - +
128D ARG* 2.9 45.1 + - + +
143D ILE* 3.4 33.9 - - + +
144D LEU* 1.3 79.8 - - - +
146D PRO* 1.4 67.2 - - + +
149D THR* 3.6 31.0 - - + +
150D GLY 4.1 1.6 - - - -
151D ARG* 3.7 26.7 - - + -
152D ASN 5.3 0.6 + - - -
155D GLU* 5.9 0.7 - - - +
----------------------------------------------------------
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