Contacts of the helix formed by residues 1101 - 1110 (chain A) in PDB entry 6TPG
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 SER1101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1099A MET 4.4 0.2 + - - -
1100A LEU* 1.3 74.5 - - - +
1102A ARG* 1.3 66.1 + - - +
1103A GLU* 3.7 15.9 + - - +
1104A PHE* 2.9 32.6 + - - +
1105A VAL* 3.1 12.1 + - - +
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Residues in contact with ARG1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003A ASP* 3.9 17.6 + - - +
1006A PHE* 3.3 48.8 - - + +
1007A TRP* 4.0 30.1 - - + +
1100A LEU 4.0 0.8 + - - -
1101A SER* 1.3 73.9 - - - +
1103A GLU* 1.3 63.8 + - - +
1105A VAL* 3.3 8.3 + - - +
1106A ARG* 2.8 30.1 + - - +
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Residues in contact with GLU1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A PHE* 4.0 15.9 - - + -
1101A SER* 3.2 12.4 + - - +
1102A ARG* 1.3 89.1 + - - +
1104A PHE* 1.3 57.0 + - - +
1106A ARG* 3.7 29.8 + - - +
1107A GLU* 3.0 27.2 + - - +
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Residues in contact with PHE1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A LEU* 5.7 1.3 - - + -
1026A LYS* 5.5 9.0 - - + -
1027A PHE* 4.2 17.3 - + - -
1096A ILE* 4.7 5.2 - - + -
1100A LEU* 3.3 47.8 - - + -
1101A SER* 2.9 24.6 + - - +
1103A GLU* 1.3 76.8 - - - +
1105A VAL* 1.3 59.6 + - - +
1107A GLU* 3.1 25.1 + - - +
1108A LEU* 2.9 56.1 + - + +
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Residues in contact with VAL1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A TRP* 4.3 8.5 - - + -
1036A MET* 4.5 2.9 - - + -
1038A ILE* 3.8 29.6 - - + -
1100A LEU* 4.0 23.3 - - + +
1101A SER 3.1 14.8 + - - +
1102A ARG* 3.8 7.9 - - - +
1104A PHE* 1.3 75.5 - - - +
1106A ARG* 1.3 57.8 + - - +
1108A LEU* 3.2 8.7 + - + +
1109A TYR* 2.9 59.9 + - + +
1130A GLU* 5.7 0.4 - - - +
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Residues in contact with ARG1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A PHE* 3.1 55.3 + - + -
1007A TRP* 3.7 15.4 - - + -
1008A ASN 4.2 9.2 - - - -
1011A TYR* 2.9 48.3 + - - +
1012A LEU* 4.1 3.7 - - + +
1102A ARG 2.8 17.6 + - - +
1103A GLU* 3.7 28.3 + - - +
1105A VAL* 1.3 74.3 - - - +
1107A GLU* 1.3 64.5 + - - +
1109A TYR* 3.3 1.2 + - - +
1110A GLY* 3.2 17.0 + - - -
1134A LEU* 3.5 32.2 - - + +
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Residues in contact with GLU1107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A LEU* 4.5 11.7 - - + +
1019A ARG* 5.7 4.9 - - + -
1023A LEU* 4.1 16.1 - - + +
1026A LYS* 3.3 26.9 + - - -
1103A GLU 3.0 14.1 + - - +
1104A PHE* 3.1 24.9 + - - +
1106A ARG* 1.3 78.3 - - - +
1108A LEU* 1.3 61.3 + - - +
1110A GLY* 3.1 10.7 + - - -
1111A SER* 3.3 26.0 + - - +
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Residues in contact with LEU1108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A LEU* 3.1 39.9 - - + -
1027A PHE* 4.6 6.5 - - + -
1036A MET* 4.0 15.3 - - + -
1070A ILE* 5.3 3.6 - - + -
1072A ILE* 3.4 29.6 - - + -
1096A ILE* 5.6 0.4 - - + -
1100A LEU* 4.4 1.3 - - + -
1104A PHE* 2.9 52.9 + - + +
1105A VAL* 3.5 13.2 - - + +
1107A GLU* 1.3 74.1 - - - +
1109A TYR* 1.3 63.9 + - - +
1112A VAL* 3.0 35.7 + - + +
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Residues in contact with TYR1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A TRP* 3.5 32.5 - + - -
1016A ARG* 3.0 20.8 + - - -
1036A MET* 3.2 31.6 - - + -
1038A ILE* 3.4 20.4 - - - +
1105A VAL* 2.9 24.2 + - + +
1106A ARG 3.7 2.9 - - - +
1107A GLU 3.3 0.4 - - - -
1108A LEU* 1.3 76.2 - - - +
1110A GLY* 1.3 56.4 + - - +
1112A VAL* 4.4 0.4 - - - -
1115A VAL* 4.3 7.6 - - + -
1127A VAL* 3.6 18.4 - - - +
1130A GLU* 3.8 29.2 + - + -
1131A ALA* 3.8 26.7 - - + -
1134A LEU* 3.3 24.7 - - + +
1136A ALA* 3.4 14.2 - - + +
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Residues in contact with GLY1110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A LEU* 4.0 19.3 - - - -
1016A ARG* 3.1 14.7 + - - +
1019A ARG* 2.5 28.4 + - - -
1106A ARG 3.2 8.2 + - - -
1107A GLU 3.1 6.7 + - - -
1108A LEU 3.1 0.6 - - - -
1109A TYR* 1.3 77.7 - - - +
1111A SER* 1.3 57.8 + - - +
1134A LEU* 3.6 13.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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