Contacts of the helix formed by residues 1124 - 1139 (chain M) in PDB entry 2X4Y
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 PRO1124 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110M ARG* 4.1 2.9 - - - +
1122M VAL 3.4 7.1 - - - +
1123M PRO* 1.3 88.0 - - + +
1125M LEU* 1.3 65.1 + - - +
1126M GLU* 4.1 15.0 - - + +
1127M VAL* 3.0 30.6 + - + +
1128M LEU* 3.3 9.4 + - - +
1154M TRP* 3.7 22.2 - - + +
32N THR* 4.4 5.8 - - - +
34N GLY* 5.4 6.7 - - - +
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Residues in contact with LEU1125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110M ARG* 3.4 33.5 - - - +
1124M PRO* 1.3 72.0 - - - +
1126M GLU* 1.3 57.7 + - - +
1128M LEU* 3.1 14.7 + - + +
1129M LYS* 2.9 27.3 + - - +
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Residues in contact with GLU1126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124M PRO* 3.1 10.7 - - + +
1125M LEU* 1.3 81.4 - - - +
1127M VAL* 1.3 61.7 + - + +
1129M LYS* 3.4 12.9 + - + +
1130M LEU* 2.9 29.4 + - + +
34N GLY* 5.6 5.7 - - - -
35N VAL* 5.5 7.4 + - + +
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Residues in contact with VAL1127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123M PRO* 4.3 7.6 - - + -
1124M PRO* 3.0 36.5 + - + +
1126M GLU* 1.3 82.4 - - - +
1128M LEU* 1.3 58.7 + - - +
1130M LEU* 3.2 6.6 + - - +
1131M GLY 3.0 10.6 + - - -
1144M LEU* 3.7 20.2 - - + -
1154M TRP* 4.0 23.8 - - + -
1156M TRP* 2.9 41.0 + - + +
34N GLY* 4.9 1.6 - - - -
35N VAL* 3.9 25.1 - - + +
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Residues in contact with LEU1128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106M PRO* 3.7 45.8 - - + +
1110M ARG* 3.9 28.5 - - - +
1123M PRO* 4.2 14.1 - - + -
1124M PRO 3.7 9.6 - - - +
1125M LEU* 3.1 14.3 + - + +
1127M VAL* 1.3 74.5 - - - +
1129M LYS* 1.3 64.8 + - - +
1131M GLY* 3.2 2.6 + - - -
1132M GLU* 3.1 20.8 + - - +
1144M LEU* 4.5 0.2 - - + -
1156M TRP* 4.0 14.1 - - + -
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Residues in contact with LYS1129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125M LEU 2.9 12.5 + - - +
1126M GLU* 3.5 15.7 - - + +
1127M VAL 3.4 0.2 - - - -
1128M LEU* 1.3 72.4 - - - +
1130M LEU* 1.3 67.0 + - - +
1132M GLU* 2.9 26.1 + - - +
1133M GLN* 3.0 34.3 + - + +
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Residues in contact with LEU1130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126M GLU* 2.9 19.5 + - + +
1127M VAL* 3.5 5.2 - - - +
1128M LEU 3.2 0.2 - - - -
1129M LYS* 1.3 76.2 - - - +
1131M GLY* 1.3 57.8 + - - +
1133M GLN* 3.2 22.4 + - - +
1134M MET* 2.9 57.5 + - + +
1155M GLN* 4.7 2.5 - - - +
1156M TRP* 3.7 15.7 - - + +
35N VAL* 3.9 35.2 - - + -
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Residues in contact with GLY1131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127M VAL 3.0 9.9 + - - -
1128M LEU 3.2 0.6 + - - -
1129M LYS 3.1 0.4 - - - -
1130M LEU* 1.3 74.2 - - - +
1132M GLU* 1.3 63.3 + - - +
1134M MET* 3.9 2.1 - - - +
1135M THR* 2.8 32.4 + - - -
1142M LEU* 4.6 0.3 - - - +
1156M TRP* 3.2 43.2 - - - +
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Residues in contact with GLU1132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128M LEU 3.1 11.3 + - - +
1129M LYS* 2.9 19.5 + - - +
1131M GLY* 1.3 75.9 - - - +
1133M GLN* 1.3 64.5 + - + +
1135M THR* 3.9 4.0 - - - -
1136M GLN* 3.1 39.1 + - - +
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Residues in contact with GLN1133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129M LYS* 3.0 38.7 + - + +
1130M LEU* 3.2 24.5 + - + +
1132M GLU* 1.3 80.9 - - + +
1134M MET* 1.3 58.1 + - + +
1136M GLN* 3.1 14.4 - - - +
1137M GLU* 3.0 27.8 + - - +
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Residues in contact with MET1134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130M LEU* 2.9 55.7 + - + +
1131M GLY* 4.1 1.8 - - - +
1133M GLN* 1.3 74.9 - - + +
1135M THR* 1.3 64.8 + - - +
1137M GLU* 3.2 6.8 + - - +
1138M ALA* 2.9 28.8 + - - +
1142M LEU* 3.5 14.4 - - + -
1155M GLN* 3.8 10.5 - - - +
1156M TRP* 3.8 34.1 - - + +
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Residues in contact with THR1135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131M GLY* 2.8 19.6 + - - -
1132M GLU* 3.9 4.9 - - - -
1134M MET* 1.3 75.8 - - - +
1136M GLN* 1.3 55.4 - - - +
1138M ALA* 5.0 0.2 - - - -
1139M ARG* 2.7 35.0 + - - -
1140M GLU 3.5 20.2 + - - +
1141M HIS* 4.9 2.5 - - - +
1142M LEU* 3.7 26.9 + - - +
1156M TRP* 5.1 2.6 - - - -
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Residues in contact with GLN1136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132M GLU* 3.1 27.8 + - - +
1133M GLN* 3.1 20.4 - - - +
1135M THR* 1.3 79.7 - - - +
1137M GLU* 1.3 53.5 + - - +
1139M ARG* 3.0 29.1 + - - +
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Residues in contact with GLU1137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133M GLN 3.0 15.5 + - - +
1134M MET* 3.2 7.4 + - - +
1136M GLN* 1.3 75.9 - - - +
1138M ALA* 1.3 68.7 + - + +
1139M ARG* 3.6 17.2 + - - +
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Residues in contact with ALA1138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134M MET 2.9 16.9 + - - +
1135M THR 4.9 0.2 - - - -
1137M GLU* 1.3 80.9 - - + +
1139M ARG* 1.3 73.1 + - - +
1140M GLU* 3.6 34.0 - - + +
1142M LEU* 4.9 5.4 - - + -
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Residues in contact with ARG1139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135M THR 2.7 13.8 + - - -
1136M GLN* 3.0 22.8 + - - +
1137M GLU* 3.3 18.0 + - - +
1138M ALA* 1.3 82.7 - - - +
1140M GLU* 1.3 57.6 + - - +
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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