Contacts of the helix formed by residues 1118 - 1135 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503F LEU* 3.9 37.7 - - + +
504F ARG* 4.1 17.3 - - + -
1113F PHE* 4.6 21.5 - - + +
1116F THR 3.8 0.8 + - - -
1117F PRO* 1.3 71.8 - - - +
1119F GLY* 1.3 60.1 + - - +
1121F ILE* 3.1 21.9 + - + +
1122F LEU* 2.9 31.8 + - + +
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Residues in contact with GLY1119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117F PRO* 3.2 4.8 - - - +
1118F LEU* 1.3 78.4 - - - +
1120F SER* 1.3 55.0 + - - +
1122F LEU* 4.4 5.4 - - - -
1123F ASN* 2.8 49.3 + - - +
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Residues in contact with SER1120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116F THR* 5.6 2.5 - - - -
1117F PRO* 3.3 31.4 + - - +
1118F LEU 3.3 1.0 - - - -
1119F GLY* 1.3 75.5 - - - +
1121F ILE* 1.3 52.5 + - - +
1123F ASN* 4.5 2.7 - - - +
1124F ARG* 2.5 46.9 + - - +
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Residues in contact with ILE1121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F LEU* 6.0 6.1 - - + -
1105F ILE* 6.0 6.5 - - + -
1112F PHE 5.6 0.2 - - - +
1113F PHE* 5.2 10.1 - - + -
1116F THR* 5.0 12.3 - - - -
1117F PRO 3.7 15.7 - - - +
1118F LEU* 3.1 27.1 + - + +
1119F GLY 3.1 0.6 - - - -
1120F SER* 1.3 78.9 - - - +
1122F LEU* 1.3 61.4 + - - +
1123F ASN 3.3 0.4 - - - -
1124F ARG* 3.2 28.0 + - - +
1125F PHE* 2.9 27.5 + - + +
1319F LEU* 5.7 9.0 - - + -
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Residues in contact with LEU1122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F LEU* 4.2 19.5 - - + +
499F THR* 4.4 8.5 - - - -
500F ASN* 4.2 25.1 - - + +
1118F LEU* 2.9 17.3 + - + +
1119F GLY* 4.3 4.3 - - - +
1121F ILE* 1.3 75.7 - - + +
1123F ASN* 1.3 61.6 + - - +
1125F PHE* 3.4 25.5 - - + +
1126F SER* 2.9 31.7 + - - -
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Residues in contact with ASN1123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119F GLY* 2.8 33.1 + - - +
1120F SER* 4.9 3.1 - - - +
1122F LEU* 1.3 78.3 - - - +
1124F ARG* 1.3 53.0 + - + +
1126F SER* 4.8 3.5 - - - -
1127F SER* 2.6 42.2 + - - +
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Residues in contact with ARG1124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120F SER* 2.5 25.9 + - - +
1121F ILE* 3.2 40.7 + - - +
1123F ASN* 1.3 78.2 - - + +
1125F PHE* 1.3 57.5 + - - +
1127F SER* 4.0 0.2 - - - -
1128F ASP* 2.9 53.5 + - - +
1129F CYS 3.7 0.9 + - - -
1314F ARG* 3.5 46.4 + - - +
1315F ILE* 4.2 9.5 - - + +
1317F ALA* 3.6 19.6 + - - +
1319F LEU* 5.8 10.3 - - - +
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Residues in contact with PHE1125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492F SER 5.7 0.2 - - - -
495F ARG* 4.4 15.9 - - + -
496F LEU* 3.8 28.5 - - + -
499F THR* 3.9 15.7 - - - -
1121F ILE* 2.9 16.4 + - + +
1122F LEU* 3.2 27.1 + - + +
1124F ARG* 1.3 74.6 - - - +
1126F SER* 1.3 62.9 + - - +
1129F CYS* 3.2 35.3 - - + +
1315F ILE* 5.4 3.6 - - - -
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Residues in contact with SER1126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496F LEU* 5.3 9.9 - - - +
1122F LEU* 2.9 19.8 + - - -
1123F ASN* 4.2 3.6 - - - -
1125F PHE* 1.3 81.5 - - - +
1127F SER* 1.3 66.2 + - - +
1129F CYS* 3.2 4.6 - - - -
1130F ASN* 2.9 41.7 + - - +
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Residues in contact with SER1127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123F ASN* 2.6 29.4 + - - +
1126F SER* 1.3 75.4 - - - +
1128F ASP* 1.3 78.4 + - - +
1130F ASN* 3.3 6.5 + - - +
1131F THR* 2.7 34.6 + - - -
1314F ARG* 4.2 5.3 + - - -
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Residues in contact with ASP1128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124F ARG* 2.9 33.6 + - - +
1127F SER* 1.3 85.5 + - - +
1129F CYS* 1.3 57.7 + - - +
1131F THR* 3.3 1.4 + - - -
1132F ILE* 2.9 36.5 + - - +
1311F ALA* 3.3 18.1 - - + +
1314F ARG* 2.4 54.6 + - - +
1315F ILE* 3.6 20.0 - - + +
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Residues in contact with CYS1129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492F SER* 6.5 0.7 - - - -
1124F ARG 3.7 3.2 + - - -
1125F PHE* 3.2 30.5 - - + +
1126F SER* 3.2 8.0 + - - -
1127F SER 3.3 0.2 - - - -
1128F ASP* 1.3 79.3 - - - +
1130F ASN* 1.3 74.5 + - - +
1132F ILE* 3.3 6.6 + - - +
1133F ASP* 2.9 46.7 + - - +
1315F ILE* 5.2 2.6 - - + +
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Residues in contact with ASN1130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488F THR* 6.1 1.2 - - - +
492F SER* 4.8 15.6 - - - -
1126F SER* 2.9 35.1 + - - +
1127F SER* 3.8 4.6 - - - +
1129F CYS* 1.3 90.6 - - - +
1131F THR* 1.3 57.9 + - - +
1133F ASP* 4.8 1.9 - - - +
1134F GLN* 2.9 46.4 + - + +
1135F HIS* 4.2 2.8 - - - -
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Residues in contact with THR1131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127F SER* 2.7 23.8 + - - -
1128F ASP* 3.5 9.2 - - - -
1130F ASN* 1.3 76.3 - - - +
1132F ILE* 1.3 58.5 + - - +
1135F HIS* 2.9 35.7 + - + -
1136F ILE* 3.2 18.0 + - + -
1308F GLN* 3.6 46.0 - - + +
1311F ALA* 4.2 8.2 - - + +
1314F ARG* 5.6 0.5 + - - -
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Residues in contact with ILE1132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090F GLY* 5.5 3.0 - - - +
1093F VAL* 5.4 7.4 - - + -
1094F ALA* 4.9 13.2 - - + +
1097F LEU* 5.7 8.1 - - + -
1128F ASP 2.9 25.8 + - - +
1129F CYS* 3.9 4.0 - - - +
1131F THR* 1.3 75.5 - - - +
1133F ASP* 1.3 70.5 + - - +
1136F ILE* 3.8 14.8 - - + +
1137F PRO* 3.3 27.2 - - - +
1311F ALA* 5.0 0.7 - - + -
1312F VAL* 3.7 38.4 - - + +
1315F ILE* 4.2 20.6 - - + -
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Residues in contact with ASP1133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533F LEU* 5.6 12.9 - - + +
536F PHE* 5.4 5.7 - - - +
1090F GLY 5.0 0.3 - - - +
1094F ALA* 3.3 32.3 - - + +
1129F CYS* 2.9 30.9 + - - +
1130F ASN* 4.5 2.5 - - - +
1132F ILE* 1.3 90.2 - - - +
1134F GLN* 1.3 78.0 + - - +
1137F PRO* 4.8 4.7 - - - +
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Residues in contact with GLN1134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485F GLN* 3.6 27.6 + - - +
488F THR* 4.1 24.0 + - - +
533F LEU* 6.0 3.4 - - - +
536F PHE* 5.2 12.4 - - - +
1130F ASN* 2.9 30.5 + - + +
1132F ILE 3.4 0.2 - - - -
1133F ASP* 1.3 98.1 + - - +
1135F HIS* 1.3 83.0 + - + +
1136F ILE 3.9 0.4 - - - -
1137F PRO* 4.3 5.3 - - - +
1138F SER* 4.2 9.5 + - - -
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Residues in contact with HIS1135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130F ASN 4.2 6.7 - - - -
1131F THR* 2.9 12.3 + - - +
1134F GLN* 1.3 99.1 + - + +
1136F ILE* 1.3 66.0 - - - +
1137F PRO 3.5 1.1 - - - -
1138F SER* 3.5 4.3 + - - -
1139F THR* 2.7 33.4 + - - +
1304F ASP* 5.8 0.2 - - - +
1308F GLN* 3.4 29.6 - - - +
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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