Contacts of the helix formed by residues 1136 - 1145 (chain J) in PDB entry 4XLN
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 LYS1136 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124J GLN* 5.0 2.9 - - - +
1134J LEU* 3.3 6.5 + - - -
1135J ARG* 1.3 74.5 - - - +
1137J ARG* 1.3 72.8 + - - +
1138J SER* 3.8 17.0 - - - +
1139J ASP* 2.8 43.9 + - - +
1140J ILE 3.4 1.4 + - - -
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Residues in contact with ARG1137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134J LEU* 5.4 2.1 - - + +
1135J ARG 3.5 3.1 + - - -
1136J LYS* 1.3 89.0 - - + +
1138J SER* 1.3 58.4 + - - +
1139J ASP 3.3 0.2 - - - -
1140J ILE* 3.8 3.2 - - - +
1141J GLU* 2.9 48.0 + - + +
1172J HIS* 3.8 27.4 - - - +
1175J ILE* 3.9 24.9 - - + -
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Residues in contact with SER1138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136J LYS* 2.8 18.1 + - - +
1137J ARG* 1.3 77.5 - - - +
1139J ASP* 1.3 68.8 + - - +
1141J GLU* 3.4 10.6 + - - +
1142J SER* 2.9 29.3 + - - -
1362J LYS* 3.8 36.1 - - - +
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Residues in contact with ASP1139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124J GLN* 4.4 11.4 + - - +
1135J ARG* 4.1 22.6 + - + +
1136J LYS* 2.8 33.4 + - - +
1138J SER* 1.3 80.4 + - - +
1140J ILE* 1.3 56.0 + - - +
1142J SER* 2.5 23.3 + - - -
1143J GLY* 2.9 13.3 + - - -
1357J ARG* 3.2 47.9 + - - +
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Residues in contact with ILE1140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120J VAL* 6.6 0.7 - - - -
1122J LEU* 3.9 39.7 - - + +
1134J LEU* 3.9 16.6 - - + -
1135J ARG* 3.2 40.2 - - + +
1136J LYS 3.4 2.1 + - - +
1137J ARG 4.0 4.9 - - - +
1139J ASP* 1.3 73.0 - - - +
1141J GLU* 1.3 60.7 + - - +
1143J GLY* 4.4 1.1 - - - +
1144J LEU* 2.9 40.1 + - + +
1171J VAL* 3.6 17.7 - - + +
1175J ILE* 3.8 24.9 - - + -
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Residues in contact with GLU1141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776J GLU* 3.4 29.3 - - - +
1137J ARG* 2.9 49.5 + - + +
1138J SER* 3.5 9.1 - - - +
1140J ILE* 1.3 76.1 - - - +
1142J SER* 1.3 60.0 + - - +
1143J GLY 3.1 0.2 + - - -
1145J TYR* 2.8 42.0 + - + +
1168J LEU* 3.6 28.5 - - + +
1171J VAL* 4.1 9.6 - - + +
1172J HIS* 3.9 5.9 + - + +
1362J LYS* 4.3 13.7 + - + +
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Residues in contact with SER1142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774J SER 6.1 1.1 - - - -
1138J SER 2.9 15.4 + - - -
1139J ASP* 2.5 26.3 + - - -
1141J GLU* 1.3 75.3 - - - +
1143J GLY* 1.3 51.9 + - - +
1145J TYR* 5.4 0.2 - - - -
1353J GLN* 3.8 4.2 + - - -
1357J ARG* 3.2 12.5 + - - -
1362J LYS* 4.5 11.6 - - - +
1363J LEU 3.2 26.7 - - - -
1364J HIS* 2.3 40.3 + - - +
1365J ASP* 3.1 8.0 + - - -
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Residues in contact with GLY1143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120J VAL* 4.8 11.4 - - - +
1135J ARG* 5.8 1.1 - - - -
1139J ASP 2.9 13.9 + - - -
1140J ILE* 3.8 1.6 - - - -
1142J SER* 1.3 78.4 + - - +
1144J LEU* 1.3 67.7 + - - +
1147J ARG* 3.1 24.1 + - - +
1357J ARG* 5.3 0.2 - - - -
1364J HIS* 3.1 8.0 - - - -
1365J ASP* 3.5 19.5 - - - +
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Residues in contact with LEU1144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120J VAL* 3.7 38.1 - - + +
1122J LEU* 4.7 3.4 - - + -
1140J ILE* 2.9 34.9 + - + +
1143J GLY* 1.3 78.5 - - - +
1145J TYR* 1.3 64.2 + - - +
1146J GLY 3.3 1.0 + - - -
1147J ARG* 3.2 19.0 + - - +
1166J LEU* 3.6 12.5 - - + +
1171J VAL* 3.6 20.0 - - + +
1174J LEU* 3.7 20.2 - - + -
1186J VAL* 3.6 36.8 - - + -
1188J VAL* 4.5 5.2 - - + -
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Residues in contact with TYR1145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770J LEU* 4.9 0.2 - - - +
774J SER 4.3 12.8 - - - -
775J GLY* 4.1 26.3 + - - -
776J GLU* 4.4 10.1 - - - -
916J TYR* 2.3 40.2 + + - -
920J LEU* 5.8 0.2 - - - +
1141J GLU* 2.8 31.8 + - + +
1143J GLY 3.6 1.0 - - - -
1144J LEU* 1.3 70.6 - - - +
1146J GLY* 1.3 65.2 + - - +
1147J ARG 3.1 0.9 - - - -
1166J LEU 3.8 5.4 - - - -
1167J SER* 4.0 4.5 - - - -
1168J LEU* 3.8 28.3 - - + -
1171J VAL* 3.8 8.7 - - + +
1207J TYR* 4.1 19.7 - + - -
1209J LEU* 4.8 8.3 - - + +
1212J ALA* 4.2 16.6 - - - +
1364J HIS* 2.5 40.0 + + + +
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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