Contacts of the helix formed by residues 1231 - 1243 (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 ILE1231 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927O LEU* 3.8 24.9 - - + +
930O ASN 4.7 9.4 - - - +
931O LEU 6.4 0.4 - - - -
932O PRO* 5.9 7.6 - - + -
960O PHE* 4.6 25.1 - - + +
1227O LYS 5.9 0.2 - - - +
1228O LYS 3.5 24.9 - - - +
1229O LEU* 3.1 13.6 - - + -
1230O ASP* 1.3 76.7 - - - +
1232O ASP* 1.3 57.2 + - - +
1234O LYS* 3.0 39.4 + - + +
1235O VAL* 3.8 2.6 + - - +
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Residues in contact with ASP1232 (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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926O PRO* 5.1 8.5 - - + +
927O LEU* 3.8 28.6 - - + +
928O GLN* 5.3 1.2 - - + +
1187O PRO* 4.0 22.0 - - - +
1190O ASP* 5.7 0.5 - - - +
1191O LEU* 5.1 9.5 - - + +
1229O LEU 3.0 23.0 + - - +
1230O ASP* 3.2 8.5 - - - +
1231O ILE* 1.3 70.6 - - - +
1233O GLY* 1.3 66.3 + - - -
1234O LYS 3.2 0.4 - - - -
1235O VAL* 3.2 8.1 + - - +
1236O ILE* 2.9 29.7 + - - +
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Residues in contact with GLY1233 (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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1230O ASP* 2.8 15.8 + - - -
1232O ASP* 1.3 80.7 + - - +
1234O LYS* 1.3 56.6 + - - +
1236O ILE* 3.3 14.2 - - - +
1237O GLN 2.9 23.6 + - - -
1257O LEU* 3.3 27.5 - - - +
1261O GLU* 5.2 0.2 - - - -
1264O ARG* 5.7 0.9 - - - -
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Residues in contact with LYS1234 (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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960O PHE 4.8 12.1 + - - -
980O ILE* 4.0 41.5 - - + -
984O HIS* 3.1 23.5 - - + +
1230O ASP 4.5 4.2 + - - +
1231O ILE* 3.0 26.8 + - + +
1233O GLY* 1.3 76.6 - - - +
1235O VAL* 1.3 60.9 + - + +
1237O GLN* 3.5 1.7 + - - +
1238O ALA 2.8 19.9 + - - -
1254O LEU* 6.1 0.7 - - + -
1257O LEU* 4.0 9.9 - - + -
1258O LEU* 5.6 4.0 - - - +
1261O GLU* 2.7 42.1 + - - +
1264O ARG* 4.8 3.4 - - - +
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Residues in contact with VAL1235 (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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926O PRO* 3.7 31.0 - - + -
927O LEU* 3.8 33.7 - - + -
933O GLU* 5.0 1.6 - - - +
987O LEU* 5.9 7.6 - - + -
991O LEU* 5.3 12.3 - - + -
993O ARG* 4.2 10.8 - - - -
1231O ILE 4.4 6.3 - - - +
1232O ASP* 3.2 8.5 + - - +
1234O LYS* 1.3 77.6 - - + +
1236O ILE* 1.3 61.1 + - - +
1237O GLN 3.2 0.2 - - - -
1238O ALA* 2.9 23.5 + - + +
1239O GLY* 2.9 13.5 + - - -
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Residues in contact with ILE1236 (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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793O GLU* 5.4 2.7 - - - +
926O PRO* 5.7 0.6 - - - +
993O ARG* 3.4 37.2 - - - +
995O LEU* 3.8 25.9 - - + +
1232O ASP 2.9 11.5 + - - +
1233O GLY* 3.3 24.9 - - - +
1235O VAL* 1.3 75.1 - - - +
1237O GLN* 1.3 59.4 + - + +
1239O GLY* 3.8 6.5 + - - +
1240O LYS* 4.3 14.4 + - - +
1257O LEU* 5.2 4.9 - - + -
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Residues in contact with GLN1237 (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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984O HIS* 5.1 1.6 - - + -
1233O GLY 2.9 17.7 + - - +
1234O LYS 3.7 4.5 - - - +
1236O ILE* 1.3 77.8 - - - +
1238O ALA* 1.3 62.2 + - - +
1239O GLY 3.2 0.8 + - - -
1240O LYS* 3.5 13.0 + - - +
1241O PHE* 3.3 17.4 - - + -
1249O GLU* 2.5 39.4 + - - +
1253O LEU* 3.3 33.0 - - - +
1254O LEU* 3.6 25.3 - - + +
1256O SER* 4.5 2.3 + - - -
1257O LEU* 3.7 21.5 - - + +
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Residues in contact with ALA1238 (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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984O HIS* 3.5 16.6 - - + +
987O LEU* 5.5 9.4 - - + +
991O LEU* 6.6 0.2 - - + -
1234O LYS 2.8 16.1 + - - +
1235O VAL* 2.9 20.8 + - + +
1237O GLN* 1.3 76.5 - - - +
1239O GLY* 1.3 58.2 + - - +
1240O LYS 3.4 0.2 + - - -
1241O PHE* 3.5 21.1 + - + -
1242O ASP* 2.8 29.4 + - + +
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Residues in contact with GLY1239 (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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993O ARG* 2.9 42.0 - - - +
995O LEU* 5.7 3.8 - - - -
1235O VAL 2.9 11.5 + - - -
1236O ILE 3.8 4.2 + - - -
1237O GLN 3.2 1.4 - - - -
1238O ALA* 1.3 78.3 - - - +
1240O LYS* 1.3 57.5 + - - +
1242O ASP* 3.6 9.4 - - - -
1243O ASN* 2.9 20.4 + - - +
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Residues in contact with LYS1240 (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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995O LEU* 3.8 25.2 - - + +
997O LYS* 6.1 0.6 - - - +
998O ASP* 3.5 27.8 + - - +
1236O ILE 4.3 7.4 + - - +
1237O GLN* 3.5 11.5 + - - +
1238O ALA 3.3 1.0 - - - -
1239O GLY* 1.3 75.8 - - - +
1241O PHE* 1.3 57.6 + - - +
1243O ASN* 4.3 11.8 - - - +
1245O SER* 4.3 7.4 + - - -
1246O THR* 5.0 3.1 + - - -
1249O GLU* 3.3 41.2 - - + +
1253O LEU* 4.2 11.4 - - - -
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Residues in contact with PHE1241 (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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984O HIS* 3.2 36.3 - + + -
987O LEU 5.6 1.1 - - - -
988O ARG* 3.3 56.8 + - + +
1237O GLN* 3.3 24.2 - - + -
1238O ALA* 3.5 14.1 - - + -
1240O LYS* 1.3 75.4 - - - +
1242O ASP* 1.3 63.4 + - + +
1243O ASN 3.2 2.6 - - - +
1245O SER* 3.2 28.3 - - - +
1246O THR 4.8 0.7 - - - +
1249O GLU* 3.5 25.8 - - + -
1250O GLN* 3.5 35.0 - - + -
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Residues in contact with ASP1242 (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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987O LEU 4.4 7.1 - - - +
988O ARG* 3.3 16.6 - - - +
991O LEU* 2.9 34.9 - - - +
992O LEU* 3.1 46.1 + - - +
993O ARG* 3.4 7.8 + - - +
1238O ALA* 2.8 20.9 + - - +
1239O GLY* 3.0 11.3 + - - +
1241O PHE* 1.3 75.7 - - + +
1243O ASN* 1.3 63.8 + - - +
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Residues in contact with ASN1243 (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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992O LEU* 4.5 8.7 - - - -
993O ARG 4.0 9.1 + - - +
994O ARG* 4.7 14.1 - - + +
1239O GLY 2.9 13.6 + - - +
1240O LYS* 4.3 11.0 - - - +
1241O PHE 3.2 0.4 - - - +
1242O ASP* 1.3 81.4 - - - +
1244O LYS* 1.3 62.4 + - + +
1245O SER* 2.9 20.9 + - - +
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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