Contacts of the helix formed by residues 1118 - 1135 (chain G) in PDB entry 6BAA
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 LEU1118 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503G LEU* 3.9 37.9 - - + +
504G ARG* 4.1 17.0 - - + +
1113G PHE* 4.6 20.9 - - + +
1116G THR 3.8 1.0 + - - +
1117G PRO* 1.3 69.4 - - - +
1119G GLY* 1.3 59.7 + - - +
1121G ILE* 3.1 22.6 + - + +
1122G LEU* 2.9 31.1 + - + +
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Residues in contact with GLY1119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117G PRO* 3.2 4.3 - - - +
1118G LEU* 1.3 79.0 - - - +
1120G SER* 1.3 55.5 + - - +
1122G LEU* 4.4 5.8 - - - -
1123G ASN* 2.8 48.4 + - - +
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Residues in contact with SER1120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116G THR* 5.6 2.2 - - - -
1117G PRO* 3.3 31.3 + - - +
1118G LEU 3.3 0.2 - - - -
1119G GLY* 1.3 75.6 - - - +
1121G ILE* 1.3 53.2 + - - +
1123G ASN* 4.9 2.6 - - - +
1124G ARG* 2.5 48.0 + - - +
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Residues in contact with ILE1121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503G LEU* 6.0 6.3 - - + -
1105G ILE* 6.0 6.7 - - + -
1113G PHE* 5.2 10.8 - - + -
1116G THR* 5.0 11.2 - - - -
1117G PRO 3.7 16.4 - - - +
1118G LEU* 3.1 26.0 + - + +
1119G GLY 3.1 0.6 - - - -
1120G SER* 1.3 78.0 - - - +
1122G LEU* 1.3 61.3 + - - +
1123G ASN 3.3 0.2 - - - -
1124G ARG* 3.2 28.3 + - - +
1125G PHE* 2.9 26.8 + - + +
1319G LEU* 5.7 9.2 - - + -
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Residues in contact with LEU1122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G LEU* 4.2 20.2 - - + +
499G THR* 4.4 8.3 - - - +
500G ASN* 4.2 24.2 - - + +
1118G LEU* 2.9 16.6 + - + +
1119G GLY* 4.3 4.3 - - - +
1121G ILE* 1.3 74.9 - - - +
1123G ASN* 1.3 63.3 + - - +
1125G PHE* 3.4 25.1 - - + +
1126G SER* 2.9 31.6 + - - -
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Residues in contact with ASN1123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119G GLY* 2.8 33.1 + - - +
1120G SER* 4.9 2.8 - - - +
1122G LEU* 1.3 77.7 - - - +
1124G ARG* 1.3 52.6 + - + +
1126G SER* 4.6 3.1 - - - +
1127G SER* 2.6 43.8 + - - +
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Residues in contact with ARG1124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120G SER* 2.5 25.7 + - - +
1121G ILE* 3.2 39.5 + - - +
1123G ASN* 1.3 78.0 - - + +
1125G PHE* 1.3 59.2 + - - +
1127G SER* 4.0 0.4 - - - -
1128G ASP* 2.9 53.5 + - - +
1129G CYS 3.7 0.5 + - - -
1314G ARG* 3.5 46.9 + - - +
1315G ILE* 4.2 10.1 - - + +
1317G ALA* 3.6 19.8 + - - +
1319G LEU* 5.8 9.7 - - - +
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Residues in contact with PHE1125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495G ARG* 4.4 14.8 - - + -
496G LEU* 3.8 28.7 - - + -
499G THR* 3.9 16.2 - - - -
1121G ILE* 2.9 15.4 + - + +
1122G LEU* 3.2 27.6 + - + +
1124G ARG* 1.3 76.4 - - - +
1126G SER* 1.3 61.6 + - - +
1129G CYS* 3.2 34.5 - - + +
1315G ILE* 5.2 3.8 - - - +
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Residues in contact with SER1126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G LEU* 5.3 10.4 - - - +
1122G LEU* 2.9 19.3 + - - -
1123G ASN* 4.2 3.1 - - - -
1125G PHE* 1.3 81.8 - - - +
1127G SER* 1.3 66.2 + - - +
1129G CYS* 3.2 4.9 - - - -
1130G ASN* 2.9 41.4 + - - +
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Residues in contact with SER1127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123G ASN* 2.6 28.7 + - - +
1124G ARG* 4.0 0.3 - - - -
1126G SER* 1.3 77.0 - - - +
1128G ASP* 1.3 76.9 + - - +
1130G ASN* 3.3 5.4 + - - +
1131G THR* 2.7 34.9 + - - -
1314G ARG* 4.2 5.6 + - - -
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Residues in contact with ASP1128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124G ARG* 2.9 34.5 + - - +
1127G SER* 1.3 87.1 + - - +
1129G CYS* 1.3 57.3 + - - +
1131G THR* 3.3 1.4 + - - -
1132G ILE* 2.9 36.3 + - - +
1311G ALA* 3.5 19.3 - - + +
1314G ARG* 2.4 54.6 + - - +
1315G ILE* 3.6 19.5 - - + +
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Residues in contact with CYS1129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492G SER* 6.5 0.7 - - - -
1124G ARG 3.7 2.8 + - - -
1125G PHE* 3.2 31.9 - - + +
1126G SER* 3.2 8.7 + - - -
1127G SER 3.3 0.6 - - - -
1128G ASP* 1.3 79.3 - - - +
1130G ASN* 1.3 73.8 + - - +
1132G ILE* 3.3 6.2 + - - +
1133G ASP* 2.9 47.1 + - - +
1315G ILE* 5.2 3.0 - - + +
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Residues in contact with ASN1130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488G THR* 6.1 1.2 - - - +
492G SER* 4.8 15.7 - - - -
1126G SER* 2.9 34.8 + - - +
1127G SER* 3.8 4.8 - - - +
1129G CYS* 1.3 91.8 - - - +
1131G THR* 1.3 56.6 + - - +
1133G ASP* 4.8 2.5 - - - +
1134G GLN* 2.9 45.9 + - + +
1135G HIS* 4.2 1.7 - - - -
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Residues in contact with THR1131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127G SER* 2.7 24.0 + - - -
1128G ASP* 3.5 8.8 - - - -
1130G ASN* 1.3 76.0 - - - +
1132G ILE* 1.3 58.7 + - - +
1135G HIS* 2.9 34.2 + - - -
1136G ILE* 3.2 18.6 + - + -
1308G GLN* 3.6 46.9 - - + +
1311G ALA* 4.2 7.5 - - + +
1314G ARG* 5.6 0.9 + - - -
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Residues in contact with ILE1132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090G GLY* 5.5 2.8 - - - +
1093G VAL* 5.4 8.1 - - + +
1094G ALA* 4.9 12.8 - - + +
1097G LEU* 5.7 8.5 - - + -
1128G ASP 2.9 25.1 + - - +
1129G CYS* 3.9 4.0 - - - +
1131G THR* 1.3 75.9 - - - +
1133G ASP* 1.3 71.2 + - - +
1136G ILE* 3.8 16.3 - - + +
1137G PRO* 3.3 27.4 - - - +
1311G ALA* 5.0 0.4 - - + -
1312G VAL* 3.7 37.7 - - + +
1315G ILE* 4.2 22.0 - - + -
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Residues in contact with ASP1133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533G LEU* 5.6 12.6 - - + +
536G PHE* 5.4 5.5 - - - +
1090G GLY 5.0 0.3 - - - +
1094G ALA* 3.3 31.7 - - - +
1129G CYS* 2.9 30.9 + - - +
1130G ASN* 4.5 2.0 - - - +
1132G ILE* 1.3 88.7 - - - +
1134G GLN* 1.3 78.5 + - - +
1137G PRO* 4.8 4.3 - - - +
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Residues in contact with GLN1134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485G GLN* 3.6 27.9 + - - +
488G THR* 4.1 24.0 + - - +
533G LEU* 6.0 3.4 - - - +
536G PHE* 5.2 12.3 - - - +
1130G ASN* 2.9 31.2 + - + +
1133G ASP* 1.3 98.1 + - - +
1135G HIS* 1.3 81.1 + - + +
1136G ILE 3.9 0.7 - - - -
1137G PRO* 4.3 5.9 - - - +
1138G SER* 4.2 9.5 + - - -
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Residues in contact with HIS1135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130G ASN 4.2 7.4 - - - -
1131G THR* 2.9 11.7 + - - +
1134G GLN* 1.3 98.5 + - + +
1136G ILE* 1.3 66.5 + - - +
1137G PRO 3.5 0.9 - - - -
1138G SER* 3.5 3.8 + - - -
1139G THR* 2.7 33.3 + - - +
1304G ASP* 5.8 0.2 - - - +
1308G GLN* 3.4 28.5 - - - +
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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