Contacts of the helix formed by residues 1136 - 1145 (chain D) in PDB entry 5X22
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124D GLN* 4.8 0.6 - - - +
1133D ARG* 3.8 31.1 - - - +
1134D LEU 3.7 0.8 + - - -
1135D ARG* 1.3 76.9 - - - +
1137D ARG* 1.3 69.1 + - - +
1138D ALA* 3.5 2.7 - - + +
1139D ASP* 3.3 31.1 + - - +
1140D ILE* 3.4 9.7 + - - +
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Residues in contact with ARG1137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134D LEU* 6.4 0.4 - - - -
1135D ARG 3.6 2.1 + - - +
1136D LYS* 1.3 71.2 - - - +
1138D ALA* 1.3 65.2 + - - +
1140D ILE* 3.0 8.8 + - - +
1141D GLU* 2.9 36.5 + - - +
1172D HIS* 3.3 41.5 + - - +
1175D ILE* 3.8 43.7 - - - +
1176D LYS* 5.7 4.0 - - - +
1179D GLU* 5.6 2.6 + - - -
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Residues in contact with ALA1138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136D LYS* 3.5 2.5 - - + +
1137D ARG* 1.3 78.5 - - - +
1139D ASP* 1.3 61.3 + - - +
1141D GLU* 3.8 13.9 - - - +
1142D ALA* 2.9 28.4 + - - +
1362D LYS* 3.5 21.8 + - + +
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Residues in contact with ASP1139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124D GLN* 5.4 3.6 + - - -
1135D ARG* 3.9 29.4 + - - +
1136D LYS* 3.5 33.9 + - - +
1137D ARG 3.1 0.4 - - - -
1138D ALA* 1.3 80.6 - - - +
1140D ILE* 1.3 65.7 - - - +
1142D ALA* 3.0 9.2 + - - +
1143D GLY* 2.9 20.1 + - - -
1357D ARG* 3.2 45.5 + - - +
1365D ASP* 4.8 1.9 - - - +
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Residues in contact with ILE1140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120D VAL* 5.7 2.5 - - - -
1121D PRO 5.0 0.9 - - - +
1122D LEU* 3.6 42.4 - - + +
1134D LEU* 4.4 9.4 - - + -
1135D ARG* 3.6 45.5 - - + +
1136D LYS 3.6 8.7 - - - +
1137D ARG* 3.0 7.0 + - - +
1139D ASP* 1.3 75.5 - - - +
1141D GLU* 1.3 57.4 + - - +
1143D GLY* 3.2 2.8 + - - +
1144D LEU* 2.9 48.0 + - + +
1171D VAL* 4.3 2.0 - - + -
1175D ILE* 4.0 31.4 - - + -
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Residues in contact with GLU1141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776D GLU* 5.3 1.0 - - - +
1137D ARG* 2.9 33.0 + - - +
1138D ALA* 3.6 14.2 - - - +
1140D ILE* 1.3 76.3 - - - +
1142D ALA* 1.3 59.7 + - - +
1145D TYR* 3.0 33.5 + - + +
1168D MET* 3.6 32.2 - - + +
1171D VAL* 4.2 14.4 - - + -
1172D HIS* 3.3 19.9 + - - +
1175D ILE* 4.9 3.6 - - + -
1362D LYS* 3.5 21.5 + - - +
1364D HIS* 4.4 1.7 + - - -
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Residues in contact with ALA1142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138D ALA 2.9 19.6 + - - +
1139D ASP* 3.0 8.7 + - - +
1141D GLU* 1.3 75.9 - - - +
1143D GLY* 1.3 55.5 + - - +
1353D GLN* 5.0 2.2 - - - +
1357D ARG* 6.1 1.6 - - - +
1362D LYS* 4.1 9.4 - - + +
1363D LEU 3.7 19.7 - - - +
1364D HIS* 3.1 22.6 + - - +
1365D ASP* 3.1 36.2 + - - +
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Residues in contact with GLY1143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120D VAL* 3.4 24.1 - - - +
1135D ARG* 6.2 0.7 - - - -
1139D ASP 2.9 11.5 + - - -
1140D ILE 3.2 3.3 + - - -
1142D ALA* 1.3 76.5 - - - +
1144D LEU* 1.3 61.8 + - - +
1147D ARG* 3.2 28.9 + - - -
1365D ASP* 3.8 21.1 - - - -
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Residues in contact with LEU1144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120D VAL* 4.2 15.0 - - + -
1122D LEU* 4.0 14.8 - - + -
1140D ILE* 2.9 34.5 + - + +
1141D GLU 3.3 0.4 + - - -
1142D ALA 3.5 0.2 - - - -
1143D GLY* 1.3 86.3 - - - +
1145D TYR* 1.3 69.3 + - - +
1147D ARG* 3.0 24.2 + - - +
1166D LEU* 4.1 16.4 - - + +
1171D VAL* 3.8 18.6 - - + -
1174D LEU* 3.9 25.8 - - + -
1186D VAL* 4.0 28.9 - - + -
1188D VAL* 4.4 7.2 - - + -
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Residues in contact with TYR1145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D SER 4.9 5.4 - - - -
775D GLY* 4.4 15.6 + - - -
916D TYR* 3.1 34.8 + + - -
1141D GLU* 3.0 18.8 + - + +
1144D LEU* 1.3 77.1 - - - +
1146D GLY* 1.3 63.5 + - - +
1166D LEU 4.1 0.2 - - - -
1167D SER* 4.1 0.7 - - - -
1168D MET* 3.6 43.3 - - + -
1171D VAL* 3.6 16.4 - - + +
1207D TYR* 3.9 20.5 - + - -
1209D LEU* 3.6 29.0 + - + +
1212D ALA* 3.8 22.5 - - - +
1364D HIS* 2.7 35.2 + + - +
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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