Contacts of the helix formed by residues 1105 - 1122 (chain B) in PDB entry 3QCF
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 THR1105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852B PHE* 3.4 14.2 - - - -
1103B VAL* 4.2 0.7 - - - +
1104B GLN* 1.3 91.3 - - + +
1106B GLU* 1.3 64.3 + - - +
1107B GLU* 3.7 16.9 + - - +
1108B GLN* 3.2 35.7 + - - +
1109B TYR* 3.3 15.1 + - - +
2001B NXY 4.8 4.3 + - - +
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Residues in contact with GLU1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B GLN* 4.3 10.0 + - - +
848B PHE* 4.4 4.4 - - + +
849B SER* 2.9 46.1 + - - +
852B PHE* 3.5 32.7 - - + +
1105B THR* 1.3 70.8 - - - +
1107B GLU* 1.3 76.1 + - - +
1109B TYR* 3.0 6.0 + - + +
1110B ILE* 2.8 46.3 + - + +
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Residues in contact with GLU1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845B GLN* 5.9 0.3 + - - -
1031B VAL* 5.9 1.3 - - + -
1105B THR* 3.3 17.3 - - - +
1106B GLU* 1.3 91.2 + - - +
1108B GLN* 1.3 58.5 + - - +
1110B ILE* 3.2 14.3 + - + +
1111B PHE* 2.8 29.6 + - - +
2001B NXY 3.8 21.8 - - + +
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Residues in contact with GLN1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065B GLY* 3.4 29.8 - - - +
1066B ARG* 3.7 5.8 - - - +
1069B THR* 3.5 17.1 + - + +
1103B VAL* 4.1 5.8 - - + -
1104B GLN* 2.7 33.9 + - - +
1105B THR* 3.2 25.6 + - - +
1106B GLU 3.2 0.2 - - - -
1107B GLU* 1.3 77.2 - - - +
1109B TYR* 1.3 62.8 + - - +
1111B PHE* 3.2 7.6 + - - +
1112B ILE* 3.0 27.2 + - - +
2001B NXY 3.4 41.1 + - + -
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Residues in contact with TYR1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848B PHE* 3.9 28.3 - + + -
851B ASP* 2.8 44.8 + - + +
852B PHE* 4.0 17.0 - + + -
855B VAL* 4.8 5.2 - - + -
1088B VAL* 4.0 9.2 - - + -
1089B LEU* 3.7 19.4 - - + +
1092B LEU* 3.6 33.9 - - + -
1103B VAL* 3.8 8.0 - - + +
1105B THR 3.3 9.0 + - - +
1106B GLU* 3.0 11.7 + - + +
1108B GLN* 1.3 78.6 - - - +
1110B ILE* 1.3 62.1 + - - +
1112B ILE* 3.2 13.7 + - + +
1113B HIS* 3.0 46.2 + + - -
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Residues in contact with ILE1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B TYR* 3.7 30.2 + - + +
845B GLN* 3.4 34.1 - - - +
848B PHE* 3.6 34.1 - - + -
1106B GLU* 2.8 34.7 + - + +
1107B GLU* 3.5 14.8 - - + +
1109B TYR* 1.3 72.2 - - - +
1111B PHE* 1.3 58.8 + - - +
1113B HIS* 3.0 7.1 + - - +
1114B ASP* 3.0 23.9 + - + +
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Residues in contact with PHE1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B PRO* 4.2 16.8 - - + -
1033B GLU 5.4 1.6 - - - -
1034B TYR 4.6 2.2 - - - -
1035B ALA* 4.1 30.3 - - + -
1038B VAL* 3.9 20.9 - - + -
1069B THR* 4.1 12.8 - - + -
1073B ILE* 4.2 13.2 - - + -
1107B GLU 2.8 20.6 + - - +
1108B GLN* 3.2 4.5 + - - +
1110B ILE* 1.3 70.8 - - - +
1112B ILE* 1.3 62.1 + - - +
1114B ASP* 3.7 13.8 - - + +
1115B ALA* 2.8 31.3 + - + +
2001B NXY 3.5 58.8 - + + -
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Residues in contact with ILE1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069B THR* 3.7 20.9 - - + -
1072B VAL* 3.5 41.5 - - + -
1073B ILE* 4.1 15.8 - - + +
1088B VAL* 4.1 12.6 - - + -
1092B LEU* 5.2 0.4 - - + -
1103B VAL* 3.9 27.1 - - + -
1108B GLN 3.0 19.8 + - - +
1109B TYR* 3.2 15.0 + - + +
1111B PHE* 1.3 76.6 - - - +
1113B HIS* 1.3 55.6 + - - +
1115B ALA* 3.4 1.7 + - - +
1116B LEU* 3.0 49.7 + - + +
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Residues in contact with HIS1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833B PHE* 3.7 26.6 - + - -
836B HIS* 5.4 1.4 - - - -
837B ILE* 3.7 18.9 - - + +
840B LEU* 3.9 24.2 - - + +
841B TYR* 5.7 0.2 - - + -
848B PHE* 3.7 19.1 - + + -
851B ASP* 5.2 0.2 + - - -
1088B VAL* 3.6 36.5 - - + +
1109B TYR* 3.0 47.2 + + - -
1110B ILE 3.0 7.9 + - - +
1112B ILE* 1.3 74.8 - - - +
1114B ASP* 1.3 60.7 + - - +
1116B LEU* 3.3 5.1 + - - -
1117B LEU* 2.8 31.4 + - - +
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Residues in contact with ASP1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B TYR* 4.0 22.1 + - - +
1033B GLU 5.1 4.9 - - - +
1035B ALA* 3.8 18.8 + - - +
1110B ILE* 3.0 13.4 + - + +
1111B PHE* 3.2 18.1 + - + +
1113B HIS* 1.3 76.9 - - - +
1115B ALA* 1.3 62.1 + - - +
1117B LEU* 3.4 11.3 + - - +
1118B GLU* 3.2 36.4 + - - +
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Residues in contact with ALA1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B ALA* 3.6 23.5 - - + +
1038B VAL* 5.9 1.3 - - + -
1039B LEU* 3.4 27.9 - - + +
1073B ILE* 4.1 20.0 - - + -
1111B PHE* 2.8 23.8 + - + +
1112B ILE 3.7 4.5 - - - +
1114B ASP* 1.3 77.6 + - - +
1116B LEU* 1.3 56.1 + - - +
1118B GLU* 3.4 1.4 + - - +
1119B ALA 3.1 21.1 + - - -
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Residues in contact with LEU1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833B PHE* 4.1 18.4 - - + -
1039B LEU* 5.8 0.2 - - + -
1073B ILE* 4.2 17.0 - - + +
1076B MET* 4.0 26.0 - - + -
1077B LEU* 4.1 24.5 - - + +
1080B ILE* 4.6 7.0 - - + -
1086B VAL* 4.4 2.9 - - + -
1088B VAL* 3.8 28.9 - - + -
1112B ILE* 3.0 32.9 + - + +
1113B HIS 3.9 2.9 - - - +
1115B ALA* 1.3 74.3 - - + +
1117B LEU* 1.3 68.2 + - - +
1119B ALA* 3.3 3.4 + - - +
1120B ILE* 3.0 33.1 + - + +
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Residues in contact with LEU1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B VAL* 3.5 35.9 - - + +
837B ILE* 4.1 24.8 - - + +
841B TYR* 5.9 4.3 - - + -
1113B HIS 2.8 17.9 + - - +
1114B ASP* 3.6 13.9 - - - +
1116B LEU* 1.3 76.7 - - - +
1118B GLU* 1.3 60.5 + - + +
1120B ILE* 3.5 4.8 - - - +
1121B LEU* 2.9 50.8 + - + +
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Residues in contact with GLU1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035B ALA* 4.3 18.2 + - + +
1036B LEU* 4.3 19.0 + - + +
1039B LEU* 4.3 9.5 - - + +
1114B ASP* 3.2 26.0 + - - +
1115B ALA* 3.4 6.9 + - - +
1116B LEU 3.2 0.2 - - - -
1117B LEU* 1.3 78.7 - - + +
1119B ALA* 1.3 58.4 + - - +
1121B LEU* 3.6 8.0 - - + +
1122B GLY* 2.6 34.7 + - - -
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Residues in contact with ALA1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039B LEU* 4.0 9.8 - - + +
1043B ARG* 3.3 31.0 + - - +
1077B LEU* 3.7 24.7 - - + -
1115B ALA 3.1 17.2 + - - +
1116B LEU* 3.7 5.6 - - - +
1118B GLU* 1.3 77.6 - - - +
1120B ILE* 1.3 62.2 + - + +
1122B GLY* 3.6 13.7 + - - +
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Residues in contact with ILE1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B VAL* 3.3 36.6 - - + -
833B PHE* 3.8 28.9 - - + -
834B VAL* 4.1 17.5 - - + -
1080B ILE* 3.8 32.3 - - + -
1116B LEU 3.0 21.1 + - - +
1117B LEU* 3.5 4.3 - - - +
1119B ALA* 1.3 77.1 - - + +
1121B LEU* 1.3 65.2 + - + +
1122B GLY 3.7 4.3 - - - +
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Residues in contact with LEU1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834B VAL* 5.4 6.5 - - + -
1117B LEU* 2.9 47.0 + - + +
1118B GLU* 4.0 7.2 - - + +
1120B ILE* 1.3 77.2 - - + +
1122B GLY* 1.3 66.7 + - - +
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Residues in contact with GLY1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118B GLU 2.6 23.0 + - - -
1119B ALA* 3.6 12.3 + - - +
1120B ILE 3.3 4.9 - - - +
1121B LEU* 1.3 78.4 - - - +
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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
------------------------------------------------------------
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