Contacts of the helix formed by residues 1119 - 1133 (chain B) in PDB entry 5XA0
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 LEU1119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1116B LYS* 3.4 16.2 + - - +
1117B GLN 3.3 5.0 - - - +
1118B ASP* 1.3 80.5 - - - +
1120B ASP* 1.3 58.5 + - - +
1122B LEU* 3.8 12.2 - - - +
1123B ARG* 2.9 22.2 + - - +
1202B GLN* 3.9 19.1 - - + -
1205B LEU* 2.7 33.8 - - + +
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Residues in contact with ASP1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118B ASP 2.5 12.6 + - - +
1119B LEU* 1.3 70.3 - - - +
1121B GLN* 1.3 64.0 + - - +
1123B ARG* 2.8 16.2 + - - +
1124B SER* 3.0 12.2 + - - -
1205B LEU* 2.9 20.8 - - + +
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Residues in contact with GLN1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118B ASP* 3.3 22.5 - - + +
1120B ASP* 1.3 77.5 - - - +
1122B LEU* 1.3 62.1 + - - +
1124B SER* 3.2 11.1 + - - -
1125B ILE* 3.0 20.8 + - - +
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Residues in contact with LEU1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B ILE 5.3 2.5 - - - +
1116B LYS* 4.8 18.2 - - + -
1118B ASP* 3.9 5.6 - - + +
1119B LEU* 3.6 21.2 + - - +
1120B ASP 3.2 0.6 - - - -
1121B GLN* 1.3 78.3 - - - +
1123B ARG* 1.4 60.5 + - - +
1125B ILE* 3.0 11.0 + - - +
1126B VAL* 3.0 21.8 + - - +
1183B LEU* 5.6 0.7 - - - +
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Residues in contact with ARG1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B LEU 2.9 14.8 + - - +
1120B ASP* 2.8 14.2 + - - +
1122B LEU* 1.4 71.6 - - - +
1124B SER* 1.3 57.5 + - - +
1126B VAL* 3.4 9.1 + - - +
1127B GLU* 3.0 25.1 + - - +
1205B LEU 4.0 2.0 - - - +
1206B ARG* 4.0 28.7 - - + +
1209B GLY 6.0 0.7 - - - -
1210B ALA* 4.7 9.5 - - + -
1213B VAL* 5.4 3.1 - - - +
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Residues in contact with SER1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120B ASP 3.0 10.1 + - - -
1121B GLN* 3.2 12.5 + - - -
1123B ARG* 1.3 74.1 - - - +
1125B ILE* 1.3 60.3 + - - +
1127B GLU* 2.8 23.8 + - - +
1128B LYS* 2.9 17.1 + - - +
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Residues in contact with ILE1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121B GLN 3.0 11.7 + - - +
1122B LEU* 3.0 12.1 + - - +
1124B SER* 1.3 75.5 - - - +
1126B VAL* 1.3 57.2 + - - +
1128B LYS* 4.7 2.7 - - - +
1129B SER* 2.8 31.6 + - - -
1179B ILE* 3.8 19.2 - - + +
1183B LEU* 4.1 16.4 - - + -
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Residues in contact with VAL1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122B LEU 3.0 11.6 + - - +
1123B ARG* 3.6 11.2 - - - +
1124B SER 3.1 0.2 - - - -
1125B ILE* 1.3 78.8 - - - +
1127B GLU* 1.3 56.1 + - - +
1129B SER* 4.1 5.2 - - - -
1130B GLU* 2.8 30.2 + - - +
1134B TYR 6.5 0.7 - - - -
1183B LEU* 4.6 6.4 - - + +
1213B VAL* 4.5 2.5 - - - +
1214B VAL* 4.9 14.1 - - + -
1233B ILE* 5.7 7.2 - - + +
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Residues in contact with GLU1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123B ARG 3.0 11.9 + - - +
1124B SER* 2.8 18.8 + - - +
1126B VAL* 1.3 71.1 - - - +
1128B LYS* 1.3 58.9 + - - +
1130B GLU* 4.2 3.1 - - - +
1131B LEU* 3.0 28.3 + - - +
1213B VAL* 4.3 20.9 - - + -
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Residues in contact with LYS1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124B SER 2.9 15.9 + - - +
1125B ILE* 4.6 2.9 - - - +
1127B GLU* 1.3 68.4 - - - +
1129B SER* 1.3 70.6 + - - +
1131B LEU* 3.9 4.2 - - - +
1132B TRP* 2.8 23.7 + - - +
1176B VAL* 4.2 22.5 - - + +
1179B ILE* 5.3 3.1 - - + -
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Residues in contact with SER1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125B ILE 2.8 24.5 + - - -
1126B VAL* 4.1 4.3 - - - -
1128B LYS* 1.3 71.2 - - - +
1130B GLU* 1.3 53.7 + - - +
1132B TRP* 2.1 21.4 + - - -
1133B VAL* 2.0 51.6 + - - +
1134B TYR* 4.2 6.3 - - - -
1176B VAL 4.5 3.2 + - - -
1179B ILE* 3.5 18.9 - - - +
1180B LEU* 3.7 4.3 - - - +
1183B LEU* 4.5 2.9 - - - -
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Residues in contact with GLU1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126B VAL 2.8 27.7 + - - +
1127B GLU* 4.2 2.0 - - - +
1129B SER* 1.3 71.7 - - - +
1131B LEU* 1.3 68.4 + - - +
1132B TRP 3.7 0.2 - - - -
1133B VAL 2.8 13.8 + - - +
1134B TYR* 4.1 3.9 - - - +
1213B VAL 3.6 20.9 - - - +
1214B VAL* 4.4 5.8 - - - +
1216B GLU* 5.1 0.7 - - + -
1217B LEU* 2.4 42.0 - - + +
1233B ILE* 5.2 2.5 - - + -
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Residues in contact with LEU1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127B GLU 3.0 19.0 + - - +
1128B LYS* 3.9 6.1 - - - +
1129B SER 2.8 2.0 + - - -
1130B GLU* 1.3 78.4 - - - +
1132B TRP* 1.3 57.2 + - + +
1216B GLU* 5.7 3.2 - - - +
1217B LEU* 4.6 0.4 - - - +
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Residues in contact with TRP1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128B LYS 2.8 19.9 + - - +
1129B SER* 2.1 16.8 + - - -
1130B GLU 3.7 0.7 - - - -
1131B LEU* 1.3 71.6 - - + +
1133B VAL* 1.3 55.8 + - + +
1176B VAL* 4.4 16.4 - - + +
1177B LYS* 6.1 0.4 - - - -
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Residues in contact with VAL1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129B SER* 2.0 32.3 + - - -
1130B GLU 2.8 19.4 - - - +
1132B TRP* 1.3 69.2 - - + +
1134B TYR* 1.3 64.2 + - - +
1180B LEU* 2.7 48.2 - - + -
1217B LEU* 3.1 10.4 - - - +
1221B PRO* 5.8 2.9 - - - +
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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