Contacts of the helix formed by residues 1216 - 1229 (chain A) in PDB entry 4YKN
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 VAL1216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1214A ASP 4.5 5.6 - - - +
1215A CYS* 1.3 78.4 - - - +
1217A PRO* 1.3 75.9 - - + +
1218A GLU* 3.9 10.1 - - + +
1219A GLN* 3.2 36.6 + - + +
1220A VAL* 3.1 19.3 + - - +
1264A LYS* 3.1 30.5 - - + +
1265A TYR 4.1 7.0 - - - +
1266A PRO* 4.6 1.8 - - + -
1267A LEU* 5.1 1.1 - - - -
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Residues in contact with PRO1217 (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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1216A VAL* 1.3 92.0 - - + +
1218A GLU* 1.3 60.9 + - + +
1220A VAL* 3.1 7.7 + - + +
1221A ILE* 3.0 34.0 + - + +
1252A LEU* 3.8 22.5 - - + +
1261A PHE* 3.8 29.2 - - + +
1263A GLU 3.4 22.7 - - - +
1264A LYS* 4.5 1.6 - - - -
1265A TYR 3.5 15.0 - - - +
1267A LEU* 4.5 6.3 - - + -
1270A TYR* 4.2 4.9 - - + -
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Residues in contact with GLU1218 (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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1216A VAL* 3.3 11.0 - - + +
1217A PRO* 1.3 80.5 - - + +
1219A GLN* 1.3 58.3 + - + +
1221A ILE* 3.3 13.0 + - + +
1222A ALA 2.8 22.9 + - - -
1247A GLN* 3.1 55.0 + - + +
1290A LYS* 5.6 2.1 + - - -
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Residues in contact with GLN1219 (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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1215A CYS* 3.3 21.5 - - + +
1216A VAL* 3.2 38.8 + - + +
1217A PRO 3.2 0.6 - - - -
1218A GLU* 1.3 74.9 - - + +
1220A VAL* 1.3 65.5 + - - +
1222A ALA* 3.4 9.2 + - + +
1223A GLU* 3.1 28.3 + - + +
1247A GLN* 4.8 2.0 - - - +
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Residues in contact with VAL1220 (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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1192A VAL* 4.5 8.1 - - + -
1194A ILE* 3.9 28.7 - - + -
1209A LEU* 3.6 11.1 - - + +
1211A ILE* 4.1 7.0 - - + -
1215A CYS* 3.6 19.5 - - - -
1216A VAL 3.1 15.4 + - - +
1217A PRO* 3.1 9.1 + - + +
1219A GLN* 1.3 74.7 - - - +
1221A ILE* 1.3 66.6 + - - +
1223A GLU* 3.1 8.9 + - - +
1224A ALA* 3.1 18.0 + - - +
1252A LEU* 3.9 12.1 - - + -
1267A LEU* 4.0 22.7 - - + -
1285A LEU* 4.8 2.2 - - + -
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Residues in contact with ILE1221 (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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1194A ILE* 6.5 0.4 - - - -
1217A PRO* 3.0 22.0 + - + +
1218A GLU* 3.3 13.4 + - + +
1220A VAL* 1.3 75.1 - - - +
1222A ALA* 1.3 62.7 + - - +
1224A ALA* 3.2 10.3 + - + +
1225A ILE* 3.2 20.4 + - + +
1246A TYR* 4.0 34.8 - - + +
1247A GLN* 4.3 8.7 - - + +
1250A TYR 3.7 23.6 - - - +
1251A ILE* 4.0 15.0 - - + -
1252A LEU* 3.9 22.9 - - + -
1287A LEU* 4.0 20.4 - - + -
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Residues in contact with ALA1222 (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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1218A GLU 2.8 16.3 + - - +
1219A GLN* 3.6 10.8 - - + +
1220A VAL 3.2 0.2 - - - -
1221A ILE* 1.3 78.1 - - - +
1223A GLU* 1.3 58.2 + - + +
1225A ILE* 3.1 6.4 + - - +
1226A ARG* 2.9 25.7 + - - +
1243A VAL* 3.6 36.4 - - + +
1247A GLN* 3.7 4.2 - - - +
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Residues in contact with GLU1223 (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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1209A LEU* 4.1 12.0 - - + +
1210A LYS 5.5 1.0 - - - +
1211A ILE* 3.5 30.2 - - + +
1219A GLN 3.1 15.1 + - - +
1220A VAL 3.1 8.0 + - - +
1222A ALA* 1.3 73.5 - - + +
1224A ALA* 1.3 65.7 + - - +
1226A ARG* 3.2 37.9 + - - +
1227A LYS* 2.9 26.5 + - - +
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Residues in contact with ALA1224 (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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1194A ILE* 4.8 17.9 - - + -
1207A TYR* 5.4 11.2 - - + -
1209A LEU* 3.7 20.7 - - + +
1220A VAL 3.1 12.0 + - - +
1221A ILE* 3.2 13.4 + - + +
1223A GLU* 1.3 76.8 - - - +
1225A ILE* 1.3 64.2 + - + +
1227A LYS* 3.5 1.9 + - - +
1228A LYS* 3.1 24.1 + - - +
1287A LEU* 5.8 6.7 - - + -
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Residues in contact with ILE1225 (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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1221A ILE* 3.2 12.6 + - + +
1222A ALA 3.1 9.0 + - - +
1224A ALA* 1.3 77.2 - - + +
1226A ARG* 1.3 58.9 + - - +
1228A LYS* 4.5 6.3 - - + -
1229A THR* 2.6 42.5 + - + +
1239A LEU* 4.2 6.7 - - + -
1242A CYS* 3.7 26.0 - - + +
1243A VAL* 3.7 23.6 - - + +
1246A TYR* 3.5 58.6 - - + -
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Residues in contact with ARG1226 (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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1209A LEU* 6.0 0.2 - - - +
1222A ALA 2.9 13.7 + - - +
1223A GLU* 3.2 33.5 + - - +
1225A ILE* 1.3 77.2 - - - +
1227A LYS* 1.3 93.4 + - - +
1229A THR* 3.5 6.8 + - - -
1230A ARG* 3.3 39.0 + - - +
1239A LEU* 4.6 19.5 - - + +
1243A VAL* 6.1 0.4 - - + -
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Residues in contact with LYS1227 (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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1207A TYR* 4.7 18.2 - - + +
1208A THR* 3.3 36.3 + - - +
1209A LEU* 3.7 13.7 - - + -
1223A GLU 2.9 17.0 + - - +
1224A ALA 4.0 3.6 - - - +
1226A ARG* 1.3 95.6 - - - +
1228A LYS* 1.3 61.1 + - - +
1230A ARG* 3.4 52.8 + - - +
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Residues in contact with LYS1228 (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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1207A TYR* 3.0 44.4 + - + +
1224A ALA 3.1 18.4 + - - +
1225A ILE* 3.2 11.0 + - + +
1227A LYS* 1.3 78.9 - - - +
1229A THR* 1.3 65.2 + - + +
1230A ARG* 3.4 3.2 + - - +
1231A SER* 4.8 2.1 + - - -
1232A MET* 4.6 9.8 - - - +
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Residues in contact with THR1229 (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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1225A ILE* 2.6 36.9 + - + +
1226A ARG* 3.5 5.2 + - - -
1228A LYS* 1.3 81.2 - - + +
1230A ARG* 1.3 65.6 + - - +
1231A SER 3.2 3.4 - - - -
1232A MET* 3.0 39.2 + - - +
1233A LEU 3.9 2.9 + - - -
1234A LEU* 3.8 25.4 + - + +
1239A LEU* 3.7 15.2 - - - +
1242A CYS* 4.4 9.2 - - - -
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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