Contacts of the helix formed by residues 1124 - 1139 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110E ARG* 4.4 2.0 - - - +
1122E VAL 3.3 7.8 - - - +
1123E PRO* 1.3 87.4 - - + +
1125E LEU* 1.3 64.9 + - - +
1126E GLU* 4.1 9.0 - - + +
1127E VAL* 3.1 32.5 + - + +
1128E LEU* 3.2 11.5 + - - +
1154E TRP* 3.5 25.4 - - + +
26F ARG* 5.4 5.4 - - - +
32F THR* 4.5 6.1 - - - +
33F GLY 4.7 4.9 - - - +
34F GLY* 5.7 1.6 - - - -
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Residues in contact with LEU1125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110E ARG* 3.6 27.0 - - - +
1123E PRO 3.6 1.0 + - - -
1124E PRO* 1.3 72.2 - - - +
1126E GLU* 1.3 58.3 + - - +
1128E LEU* 3.3 14.1 + - + +
1129E LYS* 2.9 28.6 + - - +
2206E SO4 3.4 28.5 - - - +
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Residues in contact with GLU1126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124E PRO* 3.1 7.3 - - + +
1125E LEU* 1.3 78.0 - - - +
1127E VAL* 1.3 65.7 + - - +
1129E LYS* 3.4 13.7 + - + +
1130E LEU* 3.1 23.5 + - + +
34F GLY* 5.5 3.6 - - - -
35F VAL* 4.8 14.9 + - + +
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Residues in contact with VAL1127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123E PRO* 4.6 2.9 - - + -
1124E PRO* 3.1 35.0 + - + +
1126E GLU* 1.3 77.8 - - - +
1128E LEU* 1.3 59.6 + - - +
1130E LEU* 3.4 6.9 - - - +
1131E GLY 3.0 11.4 + - - -
1144E LEU* 3.6 34.5 - - + -
1154E TRP* 3.8 30.3 - - + -
1156E TRP* 2.9 29.2 + - + +
34F GLY* 4.8 2.2 - - - -
35F VAL* 4.1 22.7 - - + +
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Residues in contact with LEU1128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106E PRO* 3.7 40.8 - - + +
1110E ARG* 3.7 31.0 - - - +
1123E PRO* 4.0 15.9 - - + -
1124E PRO 3.2 11.5 + - - +
1125E LEU* 3.6 16.4 - - + +
1127E VAL* 1.3 75.8 - - - +
1129E LYS* 1.3 62.2 + - - +
1131E GLY* 3.2 2.4 + - - -
1132E GLU* 3.1 21.8 + - - +
1144E LEU* 4.5 0.4 - - + -
1156E TRP* 4.0 12.5 - - + -
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Residues in contact with LYS1129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125E LEU 2.9 17.0 + - - +
1126E GLU* 3.7 13.8 - - + +
1128E LEU* 1.3 74.5 - - - +
1130E LEU* 1.3 66.1 + - - +
1132E GLU* 3.1 12.3 + - + +
1133E GLN* 3.1 48.0 + - + +
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Residues in contact with LEU1130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126E GLU* 3.1 13.7 + - + +
1127E VAL* 3.4 9.2 - - - +
1129E LYS* 1.3 75.7 - - - +
1131E GLY* 1.3 58.5 + - - +
1133E GLN* 3.2 21.5 + - + +
1134E MET* 2.8 66.3 + - + +
1155E GLN* 4.6 0.7 - - - +
1156E TRP* 4.1 10.1 - - + -
35F VAL* 3.7 39.0 - - + -
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Residues in contact with GLY1131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127E VAL 3.0 10.5 + - - -
1128E LEU 3.2 1.1 + - - -
1129E LYS 3.1 1.0 - - - -
1130E LEU* 1.3 75.8 - - - +
1132E GLU* 1.3 57.3 + - - +
1134E MET* 4.0 1.6 - - - +
1135E THR* 2.9 36.9 + - - -
1156E TRP* 3.2 44.4 - - - +
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Residues in contact with GLU1132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107C LYS* 3.4 35.9 + - + +
1128E LEU 3.1 12.2 + - - +
1129E LYS* 3.1 13.6 + - + +
1131E GLY* 1.3 77.1 - - - +
1133E GLN* 1.3 62.8 + - + +
1135E THR* 3.9 4.3 - - - -
1136E GLN* 3.1 25.7 + - + +
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Residues in contact with GLN1133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129E LYS* 3.1 43.6 + - + +
1130E LEU* 3.6 24.0 - - + +
1132E GLU* 1.3 78.2 - - + +
1134E MET* 1.3 57.7 + - + +
1136E GLN* 3.3 16.5 + - - +
1137E GLU* 2.9 29.7 + - - +
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Residues in contact with MET1134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130E LEU* 2.8 56.7 + - + +
1131E GLY* 4.0 1.8 - - - +
1133E GLN* 1.3 72.8 - - + +
1135E THR* 1.3 57.8 + - - +
1137E GLU* 3.9 9.6 - - - +
1138E ALA* 2.9 32.1 + - - +
1142E LEU* 3.6 14.6 - - + +
1155E GLN* 3.7 20.6 - - - +
1156E TRP* 3.7 26.5 - - + +
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Residues in contact with THR1135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141C HIS* 4.2 16.1 + - + +
1131E GLY* 2.9 24.1 + - - -
1132E GLU* 3.9 4.5 - - - -
1134E MET* 1.3 75.3 - - - +
1136E GLN* 1.3 58.5 + - - +
1138E ALA 4.6 0.2 - - - +
1139E ARG* 2.7 31.9 + - - -
1140E GLU 3.5 17.7 + - - +
1141E HIS* 5.0 4.7 - - - +
1142E LEU* 3.5 24.6 + - - +
1156E TRP* 5.1 2.9 - - - -
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Residues in contact with GLN1136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105C ASP* 5.7 4.0 + - - -
1141C HIS* 5.3 4.3 - - - -
1132E GLU* 3.1 17.4 + - + +
1133E GLN* 3.6 14.9 - - - +
1135E THR* 1.3 78.9 - - - +
1137E GLU* 1.3 62.0 + - - +
1139E ARG* 3.1 25.6 + - - +
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Residues in contact with GLU1137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C PRO* 4.9 1.9 - - - +
1133E GLN 2.9 16.9 + - - +
1134E MET* 4.0 10.5 - - - +
1136E GLN* 1.3 79.8 + - - +
1138E ALA* 1.3 60.6 + - - +
1139E ARG* 3.0 26.9 + - - +
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Residues in contact with ALA1138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C PRO* 3.7 13.7 - - - +
1134E MET 2.9 18.1 + - - +
1135E THR 4.4 0.4 - - - +
1137E GLU* 1.3 78.1 - - - +
1139E ARG* 1.3 71.7 + - - +
1140E GLU* 3.9 29.4 - - + +
1142E LEU* 4.7 9.2 - - + -
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Residues in contact with ARG1139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C PRO* 3.5 25.4 + - + +
1083C LEU 2.9 30.6 + - - +
1084C ASP* 3.0 19.8 + - - +
1141C HIS* 3.4 42.1 - - + +
1143C TYR* 3.6 20.3 + - + +
1159C ARG* 5.9 2.4 - - - +
1135E THR 2.7 17.5 + - - -
1136E GLN* 3.1 19.0 + - - +
1137E GLU* 3.0 26.1 + - - +
1138E ALA* 1.3 76.1 - - - +
1140E GLU* 1.3 59.8 + - - +
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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