Contacts of the helix formed by residues 1075 - 1085 (chain A) in PDB entry 5XA0
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 LEU1075 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A CYS* 4.3 3.1 - - + -
1073A PRO* 3.1 12.4 + - + +
1074A PRO* 1.3 80.4 - - - +
1076A VAL* 1.3 54.7 + - - +
1077A SER 3.1 2.5 - - - -
1078A GLY* 3.2 15.9 - - - +
1079A ALA* 2.4 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1076 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A GLN* 5.4 2.4 - - + +
1072A TYR* 4.6 8.9 - - + +
1073A PRO 5.3 0.6 - - - -
1074A PRO* 3.6 3.0 - - - +
1075A LEU* 1.3 75.6 - - - +
1077A SER* 1.3 52.0 + - - +
1079A ALA* 2.9 11.7 - - - +
1080A LEU* 2.7 32.9 + - - +
1110A ASP* 3.6 44.0 - - + +
1111A ASN* 4.1 9.2 - - + +
1114A GLN* 5.1 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1077 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A MET 4.1 6.2 - - - +
744A CYS* 2.8 42.5 + - - -
745A LEU* 4.4 4.0 - - - -
1075A LEU 3.1 0.4 - - - -
1076A VAL* 1.3 78.1 - - - +
1078A GLY* 1.3 51.2 + - - +
1080A LEU* 2.8 13.0 + - - +
1081A GLN* 2.7 34.8 + - - +
1114A GLN* 4.7 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1078 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A MET 5.4 0.7 - - - -
744A CYS* 2.9 23.0 - - - +
1075A LEU* 2.7 20.5 + - - -
1077A SER* 1.3 70.0 - - - +
1079A ALA* 1.3 63.4 + - - +
1081A GLN* 3.1 20.0 + - - +
1082A LEU* 3.6 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1079 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075A LEU* 2.4 25.7 + - - +
1076A VAL* 2.9 16.8 - - - +
1078A GLY 1.3 66.1 - - - +
1080A LEU* 1.3 61.0 + - - +
1082A LEU* 2.9 26.0 + - - +
1083A LEU* 3.5 3.5 + - - +
1111A ASN* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1080 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076A VAL 2.7 15.9 + - - +
1077A SER* 2.8 20.0 + - - +
1079A ALA* 1.3 71.3 - - - +
1081A GLN* 1.3 62.7 + - - +
1083A LEU* 2.9 20.2 + - - +
1084A PHE* 3.5 9.5 + - - +
1111A ASN* 6.5 0.2 - - - -
1114A GLN* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1081 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ARG* 3.6 30.3 - - + -
743A MET 4.9 4.7 - - - +
1077A SER 2.7 14.5 + - - +
1078A GLY* 3.4 14.1 - - - +
1079A ALA 3.0 0.4 + - - -
1080A LEU* 1.3 74.5 - - - +
1082A LEU* 1.3 64.2 + - - +
1084A PHE* 3.0 18.8 + - - +
1085A ARG* 4.1 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1082 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039A GLY* 6.0 6.3 - - - +
1043A GLY* 6.1 1.9 - - - -
1078A GLY 3.6 3.2 + - - +
1079A ALA* 2.9 15.6 + - - +
1081A GLN* 1.3 79.2 - - - +
1083A LEU* 1.3 60.0 + - - +
1084A PHE 3.3 1.0 + - - -
1085A ARG* 3.7 13.0 + - - +
1086A HIS* 4.6 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1083 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A ALA 3.5 2.3 + - - +
1080A LEU* 2.9 17.6 + - - +
1082A LEU* 1.3 79.8 - - - +
1084A PHE* 1.3 61.4 + - - +
1085A ARG 3.4 0.9 + - - -
1086A HIS* 3.5 16.2 + - - +
1087A PHE* 4.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080A LEU 3.5 5.7 + - - +
1081A GLN* 3.0 13.4 + - - +
1083A LEU* 1.3 78.6 - - - +
1085A ARG* 1.3 64.0 + - - +
1086A HIS 3.3 0.7 + - - -
1087A PHE* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A GLY 4.9 2.7 - - - +
1043A GLY* 3.8 34.1 - - - +
1081A GLN 4.1 2.5 + - - +
1082A LEU* 3.7 8.4 + - - +
1083A LEU 3.4 1.0 - - - -
1084A PHE* 1.3 79.6 - - - +
1086A HIS* 1.3 57.3 + - - +
1087A PHE 3.2 5.0 + - - -
1088A SER* 4.1 10.4 + - - -
----------------------------------------------------------
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