Contacts of the helix formed by residues 1178 - 1191 (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 ASP1178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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962A LEU* 4.8 0.2 - - - +
1132A SER* 3.0 32.8 + - - +
1135A GLN* 2.8 32.3 + - - -
1174A PHE* 3.0 26.6 + - + +
1175A ALA 4.5 0.2 + - - -
1176A VAL 3.6 2.4 - - - +
1177A LEU* 1.3 77.5 - - - +
1179A PHE* 1.3 62.9 + - - +
1180A CYS* 3.0 6.3 + - - +
1181A TYR* 2.7 48.0 + - + +
1182A HIS* 3.2 21.1 + - - +
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Residues in contact with PHE1179 (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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956A MET* 4.1 11.2 - - + -
960A CYS* 3.5 23.3 - - - -
962A LEU* 4.2 8.5 - - + -
976A PHE* 3.3 46.7 - + + -
980A LEU* 3.9 27.1 - - + -
1124A CYS* 4.4 3.1 - - - -
1129A ARG* 3.3 43.3 - - - -
1132A SER* 3.4 38.6 - - - +
1133A ALA 3.8 8.1 - - - -
1136A PHE* 5.3 1.8 - - + -
1177A LEU 3.4 0.9 + - - -
1178A ASP* 1.3 73.3 - - - +
1180A CYS* 1.3 66.5 + - - +
1182A HIS* 3.0 6.4 + - - +
1183A LEU 3.0 18.0 + - - -
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Residues in contact with CYS1180 (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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976A PHE* 5.6 0.2 - - - -
1132A SER 4.8 1.1 - - - -
1135A GLN* 4.0 14.1 - - + +
1136A PHE* 3.4 48.9 - - - -
1139A CYS* 4.1 4.5 - - - -
1178A ASP* 3.0 9.3 + - - +
1179A PHE* 1.3 78.5 - - - +
1181A TYR* 1.3 58.4 + - - +
1183A LEU* 3.2 6.4 + - - +
1184A LEU* 2.9 30.5 + - - +
1204A MET* 4.3 0.2 - - - -
1208A ILE* 3.5 41.2 - - + +
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Residues in contact with TYR1181 (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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1135A GLN* 3.8 15.3 - - - -
1174A PHE* 3.8 20.9 - + - -
1175A ALA* 3.8 27.4 - - + +
1176A VAL 6.1 0.2 - - - +
1178A ASP* 2.7 36.7 + - + +
1179A PHE 3.3 0.2 - - - -
1180A CYS* 1.3 74.5 - - - +
1182A HIS* 1.3 56.7 + - - +
1184A LEU* 3.6 6.0 + - - +
1185A LYS* 3.0 31.6 + - - +
1208A ILE* 4.1 10.5 - - + -
1212A GLN* 3.5 51.3 + - + +
1215A ASN* 3.0 35.5 + - - +
1216A ASP* 5.0 5.9 + - - -
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Residues in contact with HIS1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A LEU* 3.8 43.4 - - + +
963A PRO* 2.7 29.9 + - + -
964A ARG* 5.5 0.2 - - - -
965A HIS* 4.5 12.8 - + - -
972A ILE* 3.9 25.4 - - + +
976A PHE* 4.3 2.2 - + - -
1178A ASP 3.2 10.7 + - - +
1179A PHE 3.0 10.4 + - - +
1181A TYR* 1.3 76.7 - - - +
1183A LEU* 1.3 65.8 + - - +
1185A LYS* 3.1 21.8 + - + +
1186A VAL* 3.0 38.9 + - + +
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Residues in contact with LEU1183 (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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969A SER* 3.4 32.5 - - - +
972A ILE* 4.2 9.6 - - + -
973A LEU* 3.8 36.3 - - + +
976A PHE* 4.3 10.8 - - + -
1136A PHE* 5.3 1.3 - - + -
1179A PHE 3.0 11.8 + - - +
1180A CYS* 3.6 9.4 - - - +
1182A HIS* 1.3 76.3 - - - +
1184A LEU* 1.3 58.2 + - - +
1186A VAL* 3.4 2.2 + - - +
1187A GLN* 2.9 32.4 + - - +
1201A LEU* 3.8 19.7 - - + -
1204A MET* 4.1 18.4 - - + -
1205A VAL* 4.1 7.6 - - + -
1208A ILE* 4.1 8.1 - - + -
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Residues in contact with LEU1184 (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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1180A CYS 2.9 17.0 + - - +
1181A TYR 3.8 4.0 - - - +
1183A LEU* 1.3 75.9 - - - +
1185A LYS* 1.3 65.7 + - - +
1187A GLN* 3.4 0.4 + - - +
1188A LYS* 3.0 53.2 + - + +
1205A VAL* 3.6 36.5 - - + +
1208A ILE* 4.1 10.1 - - + -
1209A ARG* 4.0 29.6 - - + +
1212A GLN* 3.6 31.6 - - - +
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Residues in contact with LYS1185 (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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965A HIS* 4.1 26.7 + - + +
1176A VAL* 5.1 9.1 + - - +
1181A TYR* 3.0 18.1 + - - +
1182A HIS* 3.1 23.8 + - + +
1184A LEU* 1.3 79.5 - - - +
1186A VAL* 1.3 60.8 + - - +
1188A LYS* 3.6 7.6 + - - +
1189A HIS* 3.5 17.2 + - - +
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Residues in contact with VAL1186 (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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965A HIS* 4.0 44.4 - - + +
969A SER* 3.7 14.6 - - - +
972A ILE* 3.6 27.1 - - + -
1182A HIS* 3.0 27.1 + - + +
1183A LEU 4.0 3.1 - - - +
1185A LYS* 1.3 73.5 - - + +
1187A GLN* 1.3 61.3 + - - +
1189A HIS* 2.9 22.5 + - + +
1190A ASP* 3.0 28.6 + - - +
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Residues in contact with GLN1187 (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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969A SER* 3.6 13.4 - - - +
1183A LEU 2.9 19.0 + - - +
1184A LEU 3.9 1.8 - - - +
1186A VAL* 1.3 75.9 - - - +
1188A LYS* 1.3 65.7 + - - +
1190A ASP* 3.5 7.2 - - - -
1191A GLY* 2.6 41.1 + - - -
1192A LYS 2.8 29.3 + - - +
1193A ASP* 5.0 0.6 - - - +
1201A LEU* 3.9 8.7 - - + +
1202A LYS* 4.1 27.4 + - - +
1205A VAL* 3.7 37.2 - - + +
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Residues in contact with LYS1188 (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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1184A LEU* 3.0 43.2 + - + +
1185A LYS* 3.8 7.6 - - - +
1186A VAL 3.2 0.2 - - - -
1187A GLN* 1.3 82.3 - - - +
1189A HIS* 1.3 61.8 + - - +
1191A GLY* 4.2 4.0 + - - -
1209A ARG* 6.5 0.7 - - - -
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Residues in contact with HIS1189 (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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965A HIS* 4.0 33.3 + + + +
1185A LYS 3.5 10.5 + - - +
1186A VAL* 2.9 13.1 + - - +
1188A LYS* 1.3 82.9 - - - +
1190A ASP* 1.3 69.8 + - + +
1191A GLY 3.6 0.2 + - - -
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Residues in contact with ASP1190 (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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965A HIS 4.9 0.8 - - - +
968A GLY* 3.6 7.0 - - - -
969A SER* 2.9 44.3 + - - -
1186A VAL* 3.0 17.6 + - - +
1187A GLN 3.3 5.0 - - - +
1189A HIS* 1.3 84.6 - - + +
1191A GLY* 1.3 67.0 + - - +
1192A LYS* 2.9 32.6 + - + +
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Residues in contact with GLY1191 (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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1187A GLN* 2.6 31.1 + - - -
1188A LYS* 4.2 4.0 - - - -
1189A HIS 3.3 3.2 + - - -
1190A ASP* 1.3 71.7 - - - +
1192A LYS* 1.3 63.3 + - - +
1193A ASP* 3.9 2.6 + - - +
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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