Contacts of the helix formed by residues 1155 - 1168 (chain A) in PDB entry 4N78
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 ASP1155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857A TYR* 2.9 25.4 + - + +
858A ASN* 3.9 1.4 - - - -
859A GLY* 2.8 32.4 + - - -
1150A GLU* 5.6 4.3 - - - +
1154A GLY* 1.3 72.0 - - - -
1156A GLY* 1.3 64.2 + - - +
1157A LEU 3.2 3.1 - - - -
1158A HIS* 3.0 22.1 + - - +
1159A TRP* 3.0 31.6 + - + +
1214A LEU* 4.2 27.3 - - + +
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Residues in contact with GLY1156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857A TYR* 4.4 3.0 - - - +
997A LEU 3.7 0.2 - - - +
998A ARG* 4.1 5.6 - - - -
1001A GLY* 3.2 26.7 - - - -
1002A ASN* 3.8 20.6 + - - -
1005A LEU* 4.0 16.0 - - - +
1153A PHE 4.0 4.5 + - - -
1154A GLY 3.2 2.2 - - - -
1155A ASP* 1.3 78.7 - - - +
1157A LEU* 1.3 62.0 + - - +
1159A TRP* 3.4 1.2 + - - -
1160A ALA* 3.2 9.7 + - - +
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Residues in contact with LEU1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A PHE* 3.7 38.1 - - + +
997A LEU* 3.5 30.7 - - + -
998A ARG* 4.0 12.6 - - - +
1131A TRP* 3.5 12.9 - - + -
1138A TYR* 4.6 5.6 - - + -
1149A VAL* 3.6 31.9 - - + -
1153A PHE* 4.0 20.0 + - + -
1154A GLY 3.8 6.1 + - - +
1156A GLY* 1.3 77.8 - - - +
1158A HIS* 1.3 70.9 + - + +
1160A ALA* 3.5 2.4 + - - +
1161A GLY 3.2 20.4 + - - -
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Residues in contact with HIS1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A TRP* 4.2 9.4 - - + -
1138A TYR* 3.5 36.0 + + - -
1149A VAL* 4.8 5.5 - - + +
1150A GLU* 5.6 3.6 - - + +
1154A GLY 3.9 19.2 + - - -
1155A ASP* 3.0 8.8 + - - +
1157A LEU* 1.3 84.2 - - + +
1159A TRP* 1.3 60.2 + - - +
1160A ALA 3.2 1.3 - - - -
1162A CYS* 2.9 36.0 + - - +
1211A PHE* 3.3 38.1 - + - -
1214A LEU* 3.6 22.7 - - + -
1215A ASN* 4.2 12.0 + - - +
1218A ILE* 3.8 16.2 - - + -
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Residues in contact with TRP1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857A TYR* 4.6 8.3 - + - -
859A GLY* 6.2 0.2 - - - -
1001A GLY* 4.4 11.9 - - - +
1004A ILE* 4.4 12.4 - - + +
1005A LEU* 3.5 30.2 - - + +
1008A LEU* 4.2 19.1 - - + -
1093A PHE* 4.6 5.4 - + - -
1155A ASP* 3.0 39.1 + - + +
1156A GLY* 3.4 9.8 + - - +
1158A HIS* 1.3 77.5 - - - +
1160A ALA* 1.3 57.3 + - - +
1162A CYS* 4.4 0.2 - - - +
1163A MET* 3.0 30.9 + - - +
1214A LEU* 5.5 1.4 - - - +
1217A GLU* 6.1 1.3 - - + -
1218A ILE* 3.6 40.9 - - + +
1221A ILE* 4.0 39.7 - - + -
1222A LEU* 4.1 28.1 - - + +
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Residues in contact with ALA1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A LEU* 3.0 42.6 - - + +
1000A VAL* 4.2 8.3 - - + -
1001A GLY* 3.8 9.6 - - - +
1156A GLY 3.2 6.2 + - - +
1157A LEU 3.7 7.2 - - - +
1158A HIS 3.2 0.8 - - - -
1159A TRP* 1.3 75.1 - - - +
1161A GLY* 1.3 66.0 + - - +
1163A MET* 3.1 10.7 + - + +
1164A ILE* 3.0 30.8 + - + +
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Residues in contact with GLY1161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A LEU* 4.7 1.5 - - - +
1127A PHE* 3.8 11.7 - - - -
1131A TRP* 3.6 39.2 - - - -
1157A LEU 3.2 8.5 + - - -
1158A HIS 3.5 0.2 + - - -
1160A ALA* 1.3 78.4 - - - +
1162A CYS* 1.3 59.8 + - - +
1164A ILE* 3.5 1.6 + - - -
1165A ILE* 3.2 27.9 + - - +
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Residues in contact with CYS1162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A TRP* 4.8 7.4 - - - -
1158A HIS 2.9 25.1 + - - +
1161A GLY* 1.3 73.5 - - - +
1163A MET* 1.3 60.6 + - - +
1165A ILE* 3.3 8.6 + - - +
1166A VAL* 2.8 35.3 + - - +
1174A PHE* 5.9 1.1 - - - -
1215A ASN* 3.5 37.2 - - - -
1218A ILE* 3.8 20.9 - - + -
1219A ILE* 4.0 24.9 - - + -
1222A LEU* 3.8 2.2 - - + -
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Residues in contact with MET1163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LEU* 4.9 3.1 - - + -
1000A VAL* 3.7 28.3 - - + -
1004A ILE* 3.5 34.3 - - + -
1097A LEU* 4.2 15.0 - - + -
1100A ILE* 4.1 25.6 - - + -
1104A LEU* 6.4 0.2 - - + -
1159A TRP 3.0 21.7 + - - +
1160A ALA* 3.1 11.6 + - - +
1162A CYS* 1.3 74.9 - - - +
1164A ILE* 1.3 72.0 + - + +
1166A VAL* 3.3 0.5 + - - +
1167A LEU* 2.8 49.6 + - + +
1222A LEU* 3.4 17.0 - - + +
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Residues in contact with ILE1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LEU* 4.1 21.1 - - + -
945A ILE* 5.2 0.7 - - + -
997A LEU* 4.0 21.3 - - + -
1000A VAL* 6.2 0.2 - - + -
1104A LEU* 4.2 16.4 - - + -
1109A TRP* 3.8 20.6 - - + -
1127A PHE* 3.5 42.4 - - + -
1160A ALA* 3.0 16.6 + - + +
1163A MET* 1.3 87.2 - - + +
1165A ILE* 1.3 63.5 + - - +
1167A LEU* 3.9 1.3 - - - +
1168A LEU* 3.0 42.1 + - + +
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Residues in contact with ILE1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A PHE* 3.9 17.5 - - + -
1128A HIS* 3.9 9.0 - - + -
1131A TRP* 3.5 32.8 - - + -
1161A GLY 3.2 12.7 + - - +
1162A CYS* 3.6 11.7 - - - +
1163A MET 3.2 0.2 - - - -
1164A ILE* 1.3 77.6 - - - +
1166A VAL* 1.3 59.9 + - + +
1168A LEU* 3.3 3.6 + - - -
1169A GLY 3.0 3.8 + - - -
1170A GLN* 2.8 42.0 + - + +
1171A GLN* 3.4 30.7 - - + +
1174A PHE* 3.8 27.1 - - + -
1219A ILE* 5.2 3.6 - - + -
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Residues in contact with VAL1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101A ARG* 5.4 0.7 + - - -
1162A CYS 2.8 24.6 + - - +
1163A MET 3.8 3.4 - - - +
1165A ILE* 1.3 72.4 - - - +
1167A LEU* 1.3 61.8 + - + +
1169A GLY* 2.8 20.1 + - - -
1171A GLN* 3.6 16.1 + - + +
1219A ILE* 3.8 35.4 - - + +
1222A LEU* 4.1 27.8 - - + -
1223A ASP* 4.1 16.4 - - - +
1226A LEU* 3.8 25.4 - - + +
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Residues in contact with LEU1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A LEU* 3.8 29.6 - - + +
1100A ILE* 3.7 15.0 - - + -
1101A ARG* 3.1 69.3 + - + +
1104A LEU* 4.3 11.4 - - + -
1110A ARG* 4.8 1.4 + - - -
1163A MET* 2.8 44.2 + - + +
1164A ILE 4.0 2.9 - - - +
1166A VAL* 1.3 74.6 - - + +
1168A LEU* 1.3 60.9 + - - +
1169A GLY* 3.1 1.0 + - - -
1226A LEU* 3.9 23.6 - - + -
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Residues in contact with LEU1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A LEU* 4.1 14.4 - - + -
1109A TRP* 3.7 25.8 - - + -
1110A ARG* 3.5 48.4 + - + +
1127A PHE* 3.9 10.3 - - + -
1164A ILE* 3.0 41.7 + - + +
1165A ILE 3.7 1.1 - - - +
1167A LEU* 1.3 76.9 - - - +
1169A GLY* 1.3 62.7 + - - +
1170A GLN* 3.6 38.6 + - + +
1173A ARG* 5.2 1.4 + - - -
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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