Contacts of the strand formed by residues 1135 - 1140 (chain A) in PDB entry 2XT6
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 VAL1135 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A TYR* 3.9 2.3 + - - -
1109A VAL* 4.3 2.0 - - - -
1111A ARG* 3.4 22.4 - - + +
1113A LEU* 3.7 34.3 - - + -
1127A LYS* 2.8 35.9 + - + +
1132A ARG* 3.5 31.6 + - + +
1133A GLU 3.3 0.2 - - - -
1134A ASP* 1.3 96.8 - - - +
1136A ALA* 1.3 56.6 + - - +
1137A ILE* 5.1 1.8 - - + -
1225A ALA 5.3 0.4 - - - +
1226A PHE* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A GLU* 3.4 8.3 - - - +
1099A TYR* 4.1 3.8 - - + -
1109A VAL* 3.6 24.4 - - + +
1111A ARG 3.0 6.7 + - - +
1112A LEU* 3.6 9.3 - - + +
1113A LEU* 2.9 30.3 + - - +
1135A VAL* 1.3 74.4 - - - +
1137A ILE* 1.3 63.1 + - - +
1138A VAL* 4.1 0.7 - - + -
1158A TYR* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A LEU 4.3 1.6 - - - +
1095A GLU 4.4 0.3 - - - -
1096A GLU* 2.8 51.8 + - - +
1113A LEU* 3.4 23.3 - - + +
1115A THR* 3.7 22.7 - - + -
1120A TYR* 3.5 28.2 - - + -
1123A LEU* 3.7 42.4 - - + +
1124A ALA* 3.7 13.2 - - + +
1127A LYS* 4.1 10.5 - - + -
1135A VAL* 5.1 0.9 - - + -
1136A ALA* 1.3 77.4 - - - +
1138A VAL* 1.4 64.4 - - - +
1139A ARG* 4.3 0.3 + - - -
1158A TYR* 5.4 0.5 + - - -
1226A PHE* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A VAL* 3.5 29.2 - - + -
1094A LEU 3.5 6.5 - - - +
1095A GLU* 4.7 2.9 - - + -
1112A LEU* 3.7 28.5 - - + -
1113A LEU 2.9 9.6 + - - +
1114A LEU* 3.3 11.1 - - + +
1115A THR* 2.9 27.0 + - - +
1137A ILE* 1.4 76.4 - - - +
1139A ARG* 1.3 65.2 + - - +
1151A LEU* 4.6 10.3 - - + -
1154A THR* 3.9 21.8 - - + -
1155A LEU* 4.9 1.6 - - + -
1158A TYR* 4.3 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A SER* 3.0 30.5 + - - -
1044A THR* 3.8 12.7 - - - +
1093A VAL* 3.3 9.7 - - - +
1094A LEU* 2.9 59.5 + - + +
1095A GLU 3.1 26.9 + - - -
1097A PRO* 4.2 5.9 - - - +
1115A THR* 3.3 14.1 - - + +
1116A SER* 4.8 4.7 - - - +
1117A GLY 5.1 0.2 - - - +
1120A TYR* 3.4 70.1 + - + -
1137A ILE 5.1 0.6 + - - -
1138A VAL* 1.3 75.2 - - - +
1140A ILE* 1.3 62.2 + - - +
1141A GLU* 3.6 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092A SER 3.9 3.1 - - - -
1093A VAL* 4.7 2.9 - - + +
1114A LEU* 3.6 30.5 - - + -
1115A THR 2.8 12.3 + - - +
1116A SER* 2.7 27.8 + - - -
1139A ARG* 1.3 72.1 - - - +
1141A GLU* 1.3 58.8 + - - +
1142A GLN 3.3 25.6 - - - +
1143A LEU* 3.5 17.2 - - + +
1146A LEU* 4.3 2.0 - - + -
1147A PRO* 4.3 12.1 - - + -
1151A LEU* 4.1 26.2 - - + -
1166A TRP* 3.7 18.8 - - + -
1180A PHE* 3.8 17.7 - - + -
1184A LEU* 4.6 4.3 - - + -
----------------------------------------------------------
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