Contacts of the helix formed by residues 1248 - 1263 (chain O) in PDB entry 6IY3
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 GLU1248 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246O THR* 3.2 35.0 + - - +
1247O SER* 1.3 73.3 + - - +
1249O GLU* 1.3 59.1 + - - +
1251O GLU* 3.4 9.8 - - - +
1252O ALA* 2.9 39.1 + - + +
1253O LEU* 4.0 2.9 + - + -
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Residues in contact with GLU1249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237O GLN* 2.5 28.1 + - - +
1240O LYS* 3.3 42.0 - - + +
1241O PHE* 3.5 32.5 - - + +
1246O THR* 3.2 21.1 + - - +
1247O SER 3.2 2.6 - - - -
1248O GLU* 1.3 78.1 - - - +
1250O GLN* 1.3 57.4 + - - +
1251O GLU 2.9 4.0 + - - -
1253O LEU* 2.9 54.2 + - - +
1254O LEU 2.9 7.7 + - - -
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Residues in contact with GLN1250 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981O ARG* 3.3 37.5 + - - +
984O HIS* 3.4 25.3 - - + +
985O LYS* 4.7 3.7 + - - +
988O ARG* 3.1 35.3 + - - +
1237O GLN* 5.4 0.4 - - - +
1241O PHE* 3.5 25.8 - - + -
1247O SER 4.6 1.7 + - - +
1249O GLU* 1.3 75.4 - - - +
1251O GLU* 1.3 73.3 + - - +
1254O LEU* 3.3 35.5 - - + +
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Residues in contact with GLU1251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981O ARG* 2.5 41.1 + - - +
1247O SER 2.9 25.1 - - - +
1248O GLU* 3.4 10.0 - - - +
1249O GLU 2.9 1.0 + - - -
1250O GLN* 1.3 87.7 + - - +
1252O ALA* 1.3 61.3 + - + +
1254O LEU* 3.8 2.3 - - - +
1255O ARG* 2.9 28.9 + - - +
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Residues in contact with ALA1252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248O GLU* 2.9 25.3 + - + +
1251O GLU* 1.3 75.9 - - + +
1253O LEU* 1.3 65.7 + - + +
1255O ARG* 3.0 10.4 + - - +
1256O SER* 3.0 21.8 + - - -
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Residues in contact with LEU1253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237O GLN* 3.3 14.0 - - - +
1240O LYS* 4.2 12.3 - - - -
1248O GLU* 4.0 3.1 + - + +
1249O GLU* 2.9 45.5 + - - +
1252O ALA* 1.3 80.6 - - + +
1254O LEU* 1.3 60.2 + - - +
1256O SER* 2.4 39.0 + - - +
1257O LEU 2.9 8.8 + - - -
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Residues in contact with LEU1254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977O LEU* 4.8 17.3 - - + -
980O ILE* 4.6 7.6 - - + -
981O ARG* 4.3 4.0 - - - -
984O HIS* 3.4 37.7 - - + +
1234O LYS* 6.1 0.7 - - + -
1237O GLN* 3.6 18.0 - - + +
1241O PHE* 5.4 0.2 - - + -
1249O GLU 2.9 6.3 + - - -
1250O GLN* 3.3 39.5 - - + +
1251O GLU 3.9 1.8 - - - +
1252O ALA 3.2 0.2 - - - -
1253O LEU* 1.3 77.0 - - - +
1255O ARG* 1.3 57.8 + - - +
1257O LEU* 3.2 12.2 + - + +
1258O LEU* 2.8 52.3 + - + +
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Residues in contact with ARG1255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973O GLU* 3.2 25.3 + - - +
977O LEU* 4.1 16.0 - - - +
1251O GLU 2.9 15.0 + - - +
1252O ALA* 3.0 13.9 + - - +
1254O LEU* 1.3 73.2 - - - +
1256O SER* 1.3 59.3 + - - +
1258O LEU* 3.1 31.3 + - - +
1259O ASP* 2.9 32.5 + - - +
1262O GLU* 6.2 0.7 - - - -
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Residues in contact with SER1256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237O GLN* 4.5 1.9 + - - -
1252O ALA 3.0 7.3 + - - -
1253O LEU* 2.4 46.5 + - - +
1255O ARG* 1.3 77.3 - - - +
1257O LEU* 1.3 60.2 + - - +
1259O ASP* 3.2 29.7 - - - +
1260O ALA* 3.9 2.4 + - - +
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Residues in contact with LEU1257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233O GLY* 3.3 41.7 - - - +
1234O LYS* 4.0 10.8 - - + +
1236O ILE* 5.2 4.3 - - + -
1237O GLN* 3.7 23.3 - - + +
1253O LEU 2.9 13.1 + - - +
1254O LEU* 3.3 16.6 - - + +
1256O SER* 1.3 77.6 + - - +
1258O LEU* 1.3 57.8 + - - +
1260O ALA* 2.8 32.3 + - + +
1261O GLU* 2.8 34.1 + - - +
1264O ARG* 5.3 2.2 - - - +
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Residues in contact with LEU1258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972O SER 5.8 3.4 - - - +
973O GLU* 5.0 13.5 - - + +
977O LEU* 3.8 20.9 - - + -
1234O LYS* 5.6 3.8 - - - +
1254O LEU* 2.8 32.4 + - + +
1255O ARG* 3.1 48.2 + - - +
1257O LEU* 1.3 71.4 - - + +
1259O ASP* 1.3 60.6 + - - +
1261O GLU* 3.3 29.5 - - + +
1262O GLU* 2.8 33.6 + - - +
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Residues in contact with ASP1259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255O ARG* 2.9 20.6 + - - +
1256O SER* 3.2 26.3 - - - +
1257O LEU 3.1 0.2 - - - -
1258O LEU* 1.3 76.3 - - - +
1260O ALA* 1.3 56.5 + - - +
1262O GLU* 3.2 20.8 - - - +
1263O GLU* 2.8 36.7 + - - +
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Residues in contact with ALA1260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256O SER 3.9 1.7 + - - +
1257O LEU* 2.8 26.0 + - + +
1259O ASP* 1.3 75.3 - - - +
1261O GLU* 1.3 56.2 + - - +
1263O GLU* 3.3 6.0 + - - +
1264O ARG* 3.0 46.1 + - - +
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Residues in contact with GLU1261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968O LYS* 5.9 0.9 + - - -
1230O ASP 4.4 2.4 - - - +
1234O LYS* 2.7 43.2 + - - +
1257O LEU* 2.8 46.6 + - - +
1258O LEU* 3.3 27.9 + - + +
1260O ALA* 1.3 76.4 - - - +
1262O GLU* 1.3 57.5 + - - +
1264O ARG* 3.1 48.9 + - + +
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Residues in contact with GLU1262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255O ARG* 6.2 0.5 - - - -
1258O LEU* 2.8 19.2 + - - +
1259O ASP* 3.2 33.8 - - - +
1261O GLU* 1.3 74.1 - - - +
1263O GLU* 1.3 69.6 + - - +
1264O ARG 3.2 6.3 + - - -
1265O ARG 4.3 1.7 + - - -
1266O LYS* 3.2 42.6 + - - +
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Residues in contact with GLU1263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259O ASP* 2.8 32.4 + - - +
1260O ALA* 3.4 6.5 - - - +
1262O GLU* 1.3 87.1 - - - +
1264O ARG* 1.3 65.8 + - - +
1266O LYS* 3.7 38.2 + - + +
1267O LYS* 3.6 35.3 - - + +
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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