Contacts of the helix formed by residues 1100 - 1107 (chain A) in PDB entry 3CMT
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 ASP1100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A LEU* 5.8 0.2 - - - +
1098A ALA 3.5 2.4 + - - +
1099A LEU* 1.3 78.5 - - - +
1101A PRO* 1.3 72.6 - - - +
1102A ILE* 3.2 20.5 + - - +
1103A TYR* 3.1 27.8 + - + +
1104A ALA* 2.9 20.8 + - - +
1502A ADP 3.7 8.9 + - - +
2037A VAL* 4.1 23.8 + - + +
2060A ARG* 4.7 3.8 - - - +
2250A LYS 4.3 14.1 - - - +
2251A ILE* 4.0 10.7 - - + +
2330A ASN* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A LEU* 3.4 11.4 - - - +
1100A ASP* 1.3 86.9 - - - +
1102A ILE* 1.3 74.5 + - + +
1104A ALA* 3.1 4.3 + - + +
1105A ARG* 3.0 20.8 + - - +
1111A ILE* 3.5 16.5 - - + +
2029A LEU* 3.8 35.4 - - + +
2030A GLY* 5.9 0.2 - - - -
2032A ASP 5.6 0.2 - - - +
2035A MET* 3.5 36.8 - - + +
2036A ASP* 4.5 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100A ASP* 3.2 14.9 + - - +
1101A PRO* 1.3 91.9 - - + +
1103A TYR* 1.3 62.4 + - - +
1105A ARG* 3.4 29.7 + - - +
1106A LYS* 3.1 42.8 + - - +
2036A ASP* 4.6 13.5 - - + +
2037A VAL 6.1 1.1 - - - +
2330A ASN* 4.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A THR* 3.9 17.3 + - - +
1077A LEU* 4.9 7.4 - - + -
1100A ASP* 3.1 27.5 + - + +
1102A ILE* 1.3 77.7 - - + +
1104A ALA* 1.3 67.3 + - - +
1106A LYS* 3.0 14.4 + - + +
1107A LEU* 3.0 54.1 + - + +
1262A ILE* 4.9 2.6 - - - +
1263A LEU 4.7 0.9 + - - -
1264A TYR* 4.2 4.0 - - - -
1265A GLY* 3.4 37.6 + - - -
1502A ADP 3.4 63.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A LEU* 4.2 34.3 - - + +
1099A LEU* 4.5 5.4 - - + -
1100A ASP 2.9 12.8 + - - +
1101A PRO* 3.1 12.3 + - + +
1103A TYR* 1.3 75.5 - - - +
1105A ARG* 1.3 62.5 + - - +
1107A LEU* 3.2 8.5 + - - +
1109A VAL* 3.1 28.1 + - + +
1111A ILE* 3.6 15.5 - - + -
1114A LEU* 6.3 0.2 - - + -
2029A LEU* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A PRO 3.0 8.4 + - - +
1102A ILE* 3.5 33.8 + - - +
1103A TYR 3.2 0.2 - - - -
1104A ALA* 1.3 73.0 - - - +
1106A LYS* 1.3 60.5 + - - +
1108A GLY* 2.8 21.8 + - - -
1109A VAL 3.7 13.2 - - - +
1111A ILE* 3.5 27.9 - - + +
1112A ASP* 5.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A ILE* 3.1 27.5 + - - +
1103A TYR* 3.0 22.5 + - + +
1105A ARG* 1.3 78.0 - - - +
1107A LEU* 1.3 57.9 + - - +
1108A GLY* 3.3 3.5 + - - -
1265A GLY* 3.6 37.5 - - - +
1266A GLU* 3.9 6.1 - - - +
2330A ASN* 3.3 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A THR* 3.9 20.6 - - + +
1077A LEU* 3.8 32.3 - - + -
1078A GLN* 3.0 25.1 + - - +
1081A ALA* 3.9 6.1 - - - +
1085A ARG* 5.5 0.9 + - - -
1103A TYR* 3.0 52.7 + - + +
1104A ALA* 3.6 7.9 - - - +
1105A ARG 3.1 0.6 - - - -
1106A LYS* 1.3 75.8 - - - +
1108A GLY* 1.3 60.5 + - - +
1109A VAL* 3.5 1.8 - - + -
1266A GLU 3.7 11.1 - - - +
1267A GLY* 3.5 33.9 - - - +
----------------------------------------------------------
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