Contacts of the helix formed by residues 1124 - 1139 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110O ARG* 4.5 1.3 - - - +
1122O VAL 3.4 7.6 - - - +
1123O PRO* 1.3 87.8 - - + +
1125O LEU* 1.3 66.4 + - - +
1126O GLU* 4.2 7.9 - - + +
1127O VAL* 3.0 33.0 + - + +
1128O LEU* 3.2 11.3 + - - +
1154O TRP* 3.5 25.6 - - + +
26P ARG* 5.4 5.4 - - - +
32P THR* 4.3 7.2 - - - +
33P GLY 4.9 4.0 - - - +
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Residues in contact with LEU1125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110A ARG* 3.8 23.3 - - + -
1111A GLU* 5.9 0.4 - - - +
2206A SO4 3.3 35.7 - - - +
1110O ARG* 3.7 19.6 - - - +
1123O PRO 3.7 1.4 + - - -
1124O PRO* 1.3 71.4 - - - +
1126O GLU* 1.3 56.5 + - - +
1128O LEU* 3.2 15.7 + - + +
1129O LYS* 2.9 28.2 + - - +
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Residues in contact with GLU1126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124O PRO* 3.0 6.8 - - + +
1125O LEU* 1.3 77.2 - - - +
1127O VAL* 1.3 64.5 + - + +
1129O LYS* 3.7 16.5 + - + +
1130O LEU* 3.2 20.6 + - - +
35P VAL* 5.2 4.3 - - + +
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Residues in contact with VAL1127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123O PRO* 5.0 0.9 - - + -
1124O PRO* 3.0 35.7 + - + +
1126O GLU* 1.3 75.9 - - + +
1128O LEU* 1.3 61.8 + - - +
1130O LEU* 3.1 6.5 + - - +
1131O GLY 2.9 11.6 + - - -
1144O LEU* 3.9 13.7 - - + -
1154O TRP* 3.8 35.9 - - + -
1156O TRP* 2.9 37.2 + - + +
33P GLY 5.3 0.4 - - - +
34P GLY* 4.8 1.8 - - - -
35P VAL* 3.7 25.6 - - + +
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Residues in contact with LEU1128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106O PRO* 3.8 37.9 - - + +
1107O LYS* 4.0 17.5 - - - +
1110O ARG* 3.8 27.4 - - - +
1123O PRO* 3.7 21.5 - - + -
1124O PRO 3.2 12.3 + - - +
1125O LEU* 3.5 15.5 - - + +
1127O VAL* 1.3 74.3 - - - +
1129O LYS* 1.3 65.8 + - - +
1131O GLY* 2.9 11.6 + - - -
1132O GLU* 2.9 13.6 + - - +
1144O LEU* 4.3 0.4 - - + -
1156O TRP* 3.8 15.1 - - + -
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Residues in contact with LYS1129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125O LEU 2.9 15.8 + - - +
1126O GLU* 3.8 15.7 - - + +
1127O VAL 3.3 0.2 - - - -
1128O LEU* 1.3 75.1 - - - +
1130O LEU* 1.3 62.8 + - - +
1132O GLU* 3.3 17.9 + - - +
1133O GLN* 3.0 46.4 + - + +
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Residues in contact with LEU1130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126O GLU 3.2 12.0 + - - +
1127O VAL* 3.1 11.1 + - - +
1129O LYS* 1.3 80.4 - - - +
1131O GLY* 1.3 58.0 + - - +
1133O GLN* 3.3 20.4 + - - +
1134O MET* 2.8 56.7 + - + +
1155O GLN* 5.7 0.2 - - - +
1156O TRP* 4.2 2.2 - - + +
35P VAL* 3.5 41.1 - - + -
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Residues in contact with GLY1131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127O VAL 2.9 6.7 + - - -
1128O LEU 2.9 5.8 + - - -
1130O LEU* 1.3 78.4 - - - +
1132O GLU* 1.3 51.7 + - - +
1134O MET* 3.2 1.9 + - - +
1135O THR* 2.8 41.6 + - - -
1156O TRP* 3.1 40.6 - - - +
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Residues in contact with GLU1132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128O LEU 2.9 10.5 + - - +
1129O LYS* 3.3 22.5 + - - +
1131O GLY* 1.3 74.9 - - - +
1133O GLN* 1.3 70.5 + - - +
1135O THR* 3.8 4.0 - - - -
1136O GLN* 3.0 44.9 + - + +
1156O TRP* 5.1 0.2 - - - -
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Residues in contact with GLN1133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129O LYS* 3.0 45.3 + - + +
1130O LEU* 3.4 22.3 - - + +
1132O GLU* 1.3 88.9 - - + +
1134O MET* 1.3 57.3 + - + +
1136O GLN* 3.9 5.4 - - - +
1137O GLU* 3.0 32.9 + - - +
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Residues in contact with MET1134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130O LEU* 2.8 51.0 + - + +
1131O GLY* 3.8 3.6 - - - +
1133O GLN* 1.3 73.2 - - + +
1135O THR* 1.3 60.8 + - - +
1137O GLU* 3.9 6.2 - - - +
1138O ALA* 3.0 32.1 + - - +
1142O LEU* 3.8 14.2 - - + +
1155O GLN* 3.6 24.2 - - - +
1156O TRP* 4.0 28.9 - - + +
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Residues in contact with THR1135 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1131O GLY 2.8 24.1 + - - -
1132O GLU* 3.8 4.7 - - - -
1134O MET* 1.3 74.8 - - - +
1136O GLN* 1.3 58.3 + - - +
1139O ARG* 2.8 34.5 + - - -
1140O GLU 3.5 19.0 + - - +
1141O HIS* 4.9 2.5 - - - -
1142O LEU* 3.7 27.5 + - - +
1156O TRP* 5.0 3.3 - - - -
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Residues in contact with GLN1136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1132O GLU* 3.0 36.5 + - - +
1133O GLN* 3.9 5.4 - - - +
1135O THR* 1.3 79.5 - - - +
1137O GLU* 1.3 55.6 + - - +
1139O ARG* 3.2 30.0 + - + +
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Residues in contact with GLU1137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133O GLN* 3.0 21.6 + - - +
1134O MET* 3.9 7.4 - - - +
1136O GLN* 1.3 78.3 - - - +
1138O ALA* 1.3 59.3 + - + +
1139O ARG* 2.8 26.0 + - - +
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Residues in contact with ALA1138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134O MET 3.0 18.6 + - - +
1137O GLU* 1.3 76.7 - - + +
1139O ARG* 1.3 73.9 + - - +
1140O GLU* 3.1 27.8 + - + +
1142O LEU* 5.1 5.8 - - + -
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Residues in contact with ARG1139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135O THR* 2.8 15.6 + - - +
1136O GLN* 3.2 20.0 + - + +
1137O GLU* 2.8 27.3 + - - +
1138O ALA* 1.3 79.8 - - - +
1140O GLU* 1.3 56.9 + - - +
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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