Contacts of the strand formed by residues 1032 - 1037 (chain A) in PDB entry 5J68
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 VAL1032 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A LEU* 3.8 11.7 - - + -
1027A PRO* 3.8 10.1 - - + -
1031A VAL* 1.3 85.9 - - - +
1033A SER* 1.3 60.2 + - - +
1034A LEU* 3.7 30.3 - - + -
1104A ILE* 3.4 2.8 - - - +
1105A PHE* 2.5 43.0 + - + +
1108A LEU* 3.7 23.7 - - + +
1116A PHE* 4.3 11.7 - - + -
1135A LEU* 3.7 30.3 - - + -
1137A THR* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1033 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A LEU* 3.6 10.1 - - - +
1022A SER* 3.1 38.0 + - - -
1025A VAL* 3.7 24.3 + - - +
1027A PRO* 5.4 1.0 - - - +
1031A VAL* 5.9 0.2 - - - -
1032A VAL* 1.3 75.4 - - - +
1034A LEU* 1.3 62.0 + - - +
1103A VAL 3.4 5.6 - - - -
1104A ILE* 3.7 27.8 - - - +
1244A TYR* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1034 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A LEU* 3.9 21.5 - - + -
1020A ARG 3.2 13.7 - - - +
1021A LEU* 3.6 29.8 - - + +
1022A SER 4.4 0.4 - - - +
1032A VAL* 3.7 12.3 - - + -
1033A SER* 1.3 75.2 - - - +
1035A GLU* 1.3 63.7 + - - +
1036A TRP* 5.0 0.4 - - - -
1052A LEU* 4.7 2.5 - - + -
1102A SER* 3.2 8.7 - - - -
1103A VAL* 2.7 44.9 + - + +
1105A PHE* 4.2 12.1 - - + -
1116A PHE* 3.7 40.8 - - + -
1133A VAL* 4.7 7.4 - - + -
1135A LEU* 4.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1035 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A LEU* 3.6 4.5 - - - +
1020A ARG* 2.7 45.8 + - + +
1022A SER* 3.7 21.4 + - - -
1023A PRO* 3.6 25.5 - - - +
1024A THR* 5.2 2.3 + - - +
1034A LEU* 1.3 79.4 - - - +
1036A TRP* 1.3 67.2 + - - +
1100A ILE* 4.3 18.2 - - + +
1101A TYR 3.4 7.9 - - - +
1102A SER* 4.3 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1036 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A PRO* 4.3 2.0 - - + -
1018A VAL 3.4 20.9 - - - +
1019A LEU* 3.6 18.4 - - + -
1020A ARG* 5.5 3.1 - - - +
1035A GLU* 1.3 81.0 - - - +
1037A VAL* 1.3 70.4 + - - +
1050A TYR* 3.5 51.6 - + + -
1052A LEU* 3.7 26.0 - - + -
1073A PHE* 3.9 24.7 - + - -
1077A LEU* 5.7 0.4 - - + -
1100A ILE* 3.6 6.2 - - - -
1101A TYR* 2.9 60.2 + + + +
1102A SER* 4.6 5.2 - - - -
1103A VAL* 3.7 18.6 - - + -
1118A LEU* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1037 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A PRO* 4.7 2.4 - - - +
1018A VAL* 4.6 6.9 + - + +
1020A ARG* 4.6 18.2 - - - +
1036A TRP* 1.3 82.8 - - - +
1038A ASP* 1.3 75.1 + - - +
1039A VAL* 3.4 12.5 + - + +
1094A GLU* 4.7 9.9 - - - +
1098A VAL* 4.4 16.6 - - + -
1099A SER 3.5 11.4 - - - +
1100A ILE* 3.8 18.4 - - + -
----------------------------------------------------------
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