Contacts of the helix formed by residues 1102 - 1114 (chain A) in PDB entry 6FF7
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 THR1102 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A GLU* 5.4 1.3 - - - -
971A GLY 3.9 7.0 - - - +
972A GLU* 4.1 12.8 - - - +
1084A PRO* 6.1 0.2 - - - +
1101A PHE* 1.3 78.1 - - - +
1103A ALA* 1.3 67.1 + - - +
1104A ASP 3.7 2.9 - - - -
1105A GLU* 4.5 12.6 - - - +
1106A ALA* 3.4 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A GLU 3.4 25.7 + - - +
971A GLY* 4.3 8.1 - - - -
1102A THR* 1.3 79.0 - - - +
1104A ASP* 1.3 61.6 + - + +
1106A ALA* 3.9 1.4 - - - +
1107A ARG* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A THR* 4.8 1.2 - - - -
1103A ALA* 1.3 76.9 - - + +
1105A GLU* 1.3 60.8 + - - +
1107A ARG* 3.4 7.1 + - - +
1108A ASP* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084A PRO* 6.0 6.5 - - + -
1101A PHE* 5.5 2.9 - - + -
1102A THR* 4.3 16.4 + - - +
1103A ALA 3.3 0.6 - - - -
1104A ASP* 1.3 75.5 - - - +
1106A ALA* 1.3 59.9 + - - +
1108A ASP* 3.3 5.4 + - - +
1109A LEU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A PHE* 3.7 18.7 - - + +
1102A THR 3.4 19.0 + - - +
1103A ALA* 3.5 2.8 + - - +
1104A ASP 3.4 0.2 - - - -
1105A GLU* 1.3 78.4 - - - +
1107A ARG* 1.3 58.5 + - - +
1109A LEU* 3.8 6.4 - - - +
1110A ILE* 2.9 30.5 + - - +
1149A LEU* 5.5 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103A ALA 2.9 18.8 + - - +
1104A ASP* 3.6 8.3 - - - +
1105A GLU 3.3 0.2 - - - -
1106A ALA* 1.3 76.6 - - - +
1108A ASP* 1.3 57.1 + - - +
1110A ILE* 3.4 5.3 + - - +
1111A GLN* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A ASP 2.9 17.8 + - - +
1105A GLU* 3.7 6.3 - - - +
1107A ARG* 1.3 76.1 - - - +
1109A LEU* 1.3 57.4 + - - +
1111A GLN* 3.8 4.0 - - - +
1112A ARG* 2.9 30.3 + - - +
186R ARG 5.6 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105A GLU 2.9 17.9 + - - +
1106A ALA* 3.8 6.7 - - - +
1107A ARG 3.3 0.2 - - - -
1108A ASP* 1.3 78.3 - - - +
1110A ILE* 1.3 57.7 + - - +
1112A ARG* 3.4 6.8 + - - +
1113A TYR* 3.0 27.5 + - - +
1152A ALA* 4.2 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106A ALA 2.9 17.4 + - - +
1107A ARG* 3.9 5.4 - - - +
1109A LEU* 1.3 76.8 - - - +
1111A GLN* 1.3 56.5 + - - +
1113A TYR* 3.1 3.8 + - - +
1114A LEU* 2.9 29.4 + - - +
1145A HIS 6.0 0.7 - - - +
1148A ASN* 5.0 16.8 - - + +
1149A LEU* 5.2 4.9 - - + +
1152A ALA* 4.3 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A ARG 2.9 18.0 + - - +
1108A ASP* 3.8 4.3 - - - +
1110A ILE* 1.3 75.5 - - - +
1112A ARG* 1.3 60.2 + - - +
1114A LEU* 3.8 12.5 + - - +
1115A THR* 3.9 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108A ASP 2.9 19.2 + - - +
1109A LEU* 3.7 7.6 - - - +
1111A GLN* 1.3 76.7 - - - +
1113A TYR* 1.3 64.4 + - - +
1114A LEU 3.6 0.2 + - - -
1115A THR* 3.7 14.5 + - - -
1116A GLU* 4.8 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109A LEU 3.0 14.5 + - - +
1110A ILE* 3.1 7.4 + - - +
1112A ARG* 1.3 78.3 - - - +
1114A LEU* 1.3 57.3 + - - +
1115A THR 3.2 5.4 + - - -
1116A GLU* 3.5 13.3 + - - +
1117A HIS* 3.9 11.0 + - - +
1152A ALA* 3.7 28.7 - - + +
1155A TRP* 5.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110A ILE 2.9 15.7 + - - +
1111A GLN* 3.8 9.6 + - - +
1112A ARG 3.3 0.6 - - - -
1113A TYR* 1.3 74.4 - - - +
1115A THR* 1.3 61.2 + - - +
1116A GLU 3.3 0.9 - - - -
1117A HIS* 3.9 23.1 + - - +
----------------------------------------------------------
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