Contacts of the helix formed by residues 1147 - 1156 (chain A) in PDB entry 2XT6
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 PRO1147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A SER* 3.3 39.3 - - - +
1093A VAL* 3.8 15.7 - - + -
1140A ILE* 4.3 4.7 - - + -
1142A GLN* 3.3 27.8 - - + +
1145A PRO 3.7 3.6 - - - +
1146A LEU* 1.4 89.2 - - + +
1148A ARG* 1.4 52.4 + - - +
1149A ARG 3.4 2.2 - - - -
1150A ARG* 3.1 6.9 + - + -
1151A LEU* 2.8 36.9 + - + +
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Residues in contact with ARG1148 (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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1146A LEU* 2.9 17.2 + - + +
1147A PRO* 1.4 69.1 - - - +
1149A ARG* 1.3 72.2 + - + +
1151A LEU* 3.7 2.4 + - - +
1152A ALA* 3.1 25.1 + - - +
1187A ILE* 3.0 54.3 + - + +
1188A LEU* 3.7 25.2 - - + +
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Residues in contact with ARG1149 (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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1147A PRO 3.4 1.0 - - - -
1148A ARG* 1.3 90.3 - - + +
1150A ARG* 1.4 58.4 + - - +
1152A ALA* 3.5 5.3 + - - +
1153A GLU* 3.1 35.1 + - + +
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Residues in contact with ARG1150 (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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1090A PHE 3.8 6.9 + - - -
1091A ARG* 3.3 29.9 - - - +
1092A SER* 3.2 39.2 + - - +
1093A VAL* 3.4 27.8 + - + +
1147A PRO* 3.1 10.0 + - + +
1149A ARG* 1.4 74.6 - - - +
1151A LEU* 1.4 57.3 + - - +
1153A GLU* 3.4 16.7 + - + +
1154A THR* 2.8 39.9 + - - +
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Residues in contact with LEU1151 (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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1093A VAL* 3.9 26.6 - - + +
1114A LEU* 3.8 22.4 - - + -
1138A VAL* 4.6 1.8 - - + -
1140A ILE* 4.1 19.5 - - + -
1146A LEU* 4.9 6.1 - - + -
1147A PRO* 2.8 19.4 + - + +
1148A ARG* 4.0 4.7 - - - +
1150A ARG* 1.4 74.8 - - - +
1152A ALA* 1.4 56.6 + - - +
1154A THR* 3.5 3.1 + - - -
1155A LEU* 3.0 42.6 + - + +
1184A LEU* 3.9 17.0 - - + -
1188A LEU* 4.5 5.4 - - + -
1192A PHE* 3.7 32.5 - - + -
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Residues in contact with ALA1152 (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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1148A ARG 3.1 19.2 + - - +
1149A ARG* 3.8 6.3 - - - +
1151A LEU* 1.4 73.3 - - - +
1153A GLU* 1.4 63.7 + - - +
1155A LEU 3.5 0.2 + - - -
1156A ASP* 3.1 35.7 + - - +
1188A LEU* 3.8 20.3 - - + +
1191A HIS* 3.7 20.5 + - + -
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Residues in contact with GLU1153 (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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1149A ARG* 3.1 20.8 + - - +
1150A ARG* 3.5 19.1 - - + +
1152A ALA* 1.4 75.2 - - - +
1154A THR* 1.4 61.1 + - - +
1156A ASP* 3.6 13.0 - - - +
1157A ARG* 3.4 33.1 + - - +
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Residues in contact with THR1154 (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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1093A VAL* 3.9 14.3 + - + +
1095A GLU* 3.7 32.5 - - + +
1138A VAL* 3.9 22.4 - - + -
1150A ARG* 2.8 25.5 + - - +
1151A LEU 3.6 5.8 - - - -
1153A GLU* 1.4 74.0 - - - +
1155A LEU* 1.4 66.3 + - + +
1157A ARG* 3.0 37.1 + - - +
1158A TYR* 3.3 14.7 - - + -
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Residues in contact with LEU1155 (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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1112A LEU* 3.6 30.1 - - + -
1114A LEU* 4.5 4.5 - - + -
1138A VAL* 4.9 1.8 - - + -
1151A LEU* 3.0 34.1 + - + +
1154A THR* 1.4 81.1 - - + +
1156A ASP* 1.3 61.3 + - - +
1157A ARG 3.1 0.4 - - - -
1158A TYR* 3.2 27.2 + - - +
1161A VAL* 5.0 2.9 - - - +
1164A LYS* 3.8 22.9 - - - -
1191A HIS* 3.4 29.8 - - + -
1192A PHE* 3.4 36.1 - - + -
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Residues in contact with ASP1156 (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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1152A ALA* 3.1 27.0 + - - +
1153A GLU* 3.6 10.0 - - - +
1154A THR 3.2 0.4 - - - -
1155A LEU* 1.3 73.9 - - - +
1157A ARG* 1.4 58.6 + - - +
1158A TYR 3.3 1.9 + - - -
1159A PRO* 4.5 10.9 - - - +
1191A HIS* 2.7 27.5 + - - -
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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