Contacts of the helix formed by residues 1105 - 1122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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852A PHE* 3.4 14.2 - - - -
1103A VAL* 3.9 1.2 - - - +
1104A GLN* 1.3 97.6 - - + +
1106A GLU* 1.3 59.4 + - - +
1107A GLU* 3.5 8.2 + - - +
1108A GLN* 3.0 35.8 + - - +
1109A TYR 3.0 21.8 + - - -
865B THR* 4.8 6.5 - - + -
867B GLU* 3.7 36.2 + - + +
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Residues in contact with GLU1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845A GLN* 4.6 8.1 + - - +
848A PHE* 4.2 5.9 - - + +
849A SER* 2.9 45.9 + - - +
852A PHE* 3.5 36.8 - - + +
1105A THR* 1.3 71.6 - - - +
1107A GLU* 1.3 61.3 + - - +
1109A TYR* 3.0 3.8 + - + +
1110A ILE* 2.8 49.7 + - + +
867B GLU* 5.6 1.2 - - - +
871B HIS* 6.0 1.7 + - - -
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Residues in contact with GLU1107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030A GLY* 3.2 27.6 - - - -
1031A VAL* 3.4 30.5 + - + +
1105A THR* 3.7 9.6 - - - +
1106A GLU* 1.3 80.2 - - - +
1108A GLN* 1.3 55.8 + - - +
1110A ILE* 3.5 11.5 + - - +
1111A PHE* 2.9 26.7 + - - +
867B GLU* 4.6 15.4 - - + +
872B PRO* 5.9 2.9 - - - +
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Residues in contact with GLN1108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A TRP* 5.2 3.9 - - + +
1031A VAL* 3.7 22.7 - - + +
1065A GLY* 3.4 27.9 - - - +
1066A ARG* 3.9 15.0 - - - +
1069A THR* 3.5 16.2 + - + +
1103A VAL* 4.1 5.4 - - + -
1104A GLN* 2.9 30.8 + - - +
1105A THR* 3.0 30.2 + - - +
1107A GLU* 1.3 76.1 - - - +
1109A TYR* 1.3 62.3 + - - +
1111A PHE* 3.3 4.6 + - - +
1112A ILE* 3.1 27.0 + - - +
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Residues in contact with TYR1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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848A PHE* 4.1 26.0 - + + -
851A ASP* 2.8 44.6 + - + +
852A PHE* 4.0 18.2 - + + -
855A VAL* 4.8 4.0 - - + -
1088A VAL* 3.7 17.8 - - + +
1089A LEU* 3.8 19.9 + - + +
1092A LEU* 3.6 33.4 - - + -
1103A VAL* 3.8 8.4 - - + +
1105A THR 3.0 12.6 + - - +
1106A GLU* 3.0 8.9 + - + +
1108A GLN* 1.3 73.8 - - - +
1110A ILE* 1.3 64.5 + - - +
1112A ILE* 3.3 15.2 + - + +
1113A HIS* 3.0 39.4 + + - -
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Residues in contact with ILE1110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A TYR* 3.6 31.8 + - + +
845A GLN* 3.6 31.0 - - - +
848A PHE* 3.5 35.4 - - + -
1106A GLU* 2.8 38.0 + - + +
1107A GLU* 3.7 8.7 - - - +
1109A TYR* 1.3 69.5 - - - +
1111A PHE* 1.3 67.6 + - - +
1113A HIS* 2.9 15.8 + - - +
1114A ASP* 3.1 10.2 + - + +
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Residues in contact with PHE1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026A TRP* 4.6 10.3 - + - -
1031A VAL* 4.1 22.0 - - + -
1032A PRO* 3.6 31.2 - - + -
1035A ALA* 4.0 26.2 - - + -
1038A VAL* 4.0 33.2 - - + -
1069A THR* 3.9 19.7 - - + -
1073A ILE* 4.0 19.7 - - + -
1107A GLU 2.9 15.3 + - - +
1108A GLN* 3.4 11.2 - - - +
1110A ILE* 1.3 76.1 - - - +
1112A ILE* 1.3 55.0 + - - +
1114A ASP* 3.0 14.7 + - + +
1115A ALA* 2.8 34.0 + - + +
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Residues in contact with ILE1112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1069A THR* 3.8 18.4 - - + -
1072A VAL* 3.9 31.4 - - + -
1073A ILE* 4.2 18.6 - - + +
1088A VAL* 4.3 12.6 - - + -
1092A LEU* 5.4 0.4 - - + -
1103A VAL* 3.7 35.0 - - + -
1108A GLN 3.1 20.5 + - - +
1109A TYR* 3.4 17.5 - - + +
1110A ILE 3.2 0.2 + - - -
1111A PHE* 1.3 74.8 - - - +
1113A HIS* 1.3 59.2 + - - +
1115A ALA* 3.4 2.4 + - - +
1116A LEU* 3.0 43.4 + - + +
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Residues in contact with HIS1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PHE* 3.7 26.7 - + - -
836A HIS* 5.2 1.0 - - - -
837A ILE* 3.6 24.9 - - + +
840A LEU* 3.8 17.6 - - + +
841A TYR* 5.4 0.2 - - + -
848A PHE* 3.6 21.9 - + + -
1088A VAL* 3.8 23.4 - - + +
1109A TYR* 3.0 55.6 + + - -
1110A ILE 2.9 8.5 + - - +
1112A ILE* 1.3 77.1 - - + +
1114A ASP* 1.3 65.3 + - - +
1116A LEU* 3.4 4.6 + - - +
1117A LEU* 2.9 25.1 + - - +
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Residues in contact with ASP1114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A TYR* 3.9 21.9 + - - +
1033A GLU 5.1 4.9 - - - +
1035A ALA* 3.7 21.3 + - - +
1110A ILE* 3.1 8.3 + - + +
1111A PHE* 3.0 17.5 + - + +
1113A HIS* 1.3 75.5 - - - +
1115A ALA* 1.3 62.5 + - - +
1117A LEU* 3.3 13.3 + - - +
1118A GLU* 3.1 42.0 + - - +
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Residues in contact with ALA1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035A ALA* 3.7 23.8 - - + -
1038A VAL* 6.0 0.7 - - + -
1039A LEU* 3.5 23.4 - - + +
1073A ILE* 4.0 23.8 - - + -
1111A PHE* 2.8 20.9 + - + +
1112A ILE 3.6 4.9 - - - +
1114A ASP* 1.3 78.0 + - - +
1116A LEU* 1.3 62.3 + - - +
1118A GLU 3.4 1.6 + - - -
1119A ALA* 3.1 18.7 + - - +
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Residues in contact with LEU1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PHE* 4.1 20.9 - - + -
1073A ILE* 4.3 12.8 - - + +
1076A MET* 3.8 28.9 - - + -
1077A LEU* 4.1 18.8 - - + +
1080A ILE* 3.9 19.1 - - + -
1086A VAL* 4.1 3.1 - - + -
1088A VAL* 3.7 30.1 - - + -
1112A ILE* 3.0 28.4 + - + +
1113A HIS* 3.9 4.3 - - - +
1114A ASP 3.4 0.2 - - - -
1115A ALA* 1.3 76.7 - - - +
1117A LEU* 1.3 62.5 + - - +
1119A ALA* 3.3 3.6 + - - +
1120A ILE* 3.0 30.6 + - - +
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Residues in contact with LEU1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A VAL* 3.8 36.1 - - + +
837A ILE* 3.9 27.9 - - + +
841A TYR* 5.7 2.7 - - + -
1113A HIS 2.9 18.3 + - - +
1114A ASP* 3.5 13.0 - - - +
1115A ALA 3.2 0.2 - - - -
1116A LEU* 1.3 77.4 - - - +
1118A GLU* 1.3 59.0 + - + +
1120A ILE* 3.2 4.6 + - - +
1121A LEU* 2.9 56.7 + - + +
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Residues in contact with GLU1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034A TYR* 5.6 0.5 - - - +
1035A ALA* 4.1 7.1 + - + +
1036A LEU* 3.9 24.4 + - - +
1039A LEU* 4.1 10.3 - - + -
1114A ASP* 3.1 32.1 + - - +
1115A ALA 3.8 5.8 - - - +
1117A LEU* 1.3 77.8 - - + +
1119A ALA* 1.3 56.6 + - - +
1121A LEU* 3.4 9.0 + - + +
1122A GLY* 3.0 25.5 + - - -
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Residues in contact with ALA1119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039A LEU* 3.9 4.0 - - + +
1043A ARG* 3.6 32.8 + - - +
1077A LEU* 3.8 25.8 - - + -
1080A ILE* 5.8 0.4 - - + -
1115A ALA 3.1 14.5 + - - +
1116A LEU 3.7 7.6 - - - +
1117A LEU 3.2 0.2 - - - -
1118A GLU* 1.3 77.1 - - - +
1120A ILE* 1.3 62.8 + - + +
1122A GLY* 3.3 7.6 + - - -
1123A LYS* 3.3 15.1 + - - +
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Residues in contact with ILE1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A VAL* 3.2 39.9 - - + -
833A PHE* 4.0 26.5 - - + -
834A VAL* 4.0 18.8 - - + -
1080A ILE* 4.0 30.1 - - + -
1116A LEU 3.0 23.3 + - - +
1117A LEU* 3.2 4.0 + - - +
1119A ALA* 1.3 76.6 - - - +
1121A LEU* 1.3 63.4 + - + +
1122A GLY 4.0 0.5 - - - +
1123A LYS 3.0 16.5 - - - +
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Residues in contact with LEU1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834A VAL* 5.7 4.7 - - + -
1117A LEU* 2.9 48.7 + - + +
1118A GLU* 3.9 8.1 - - + +
1120A ILE* 1.3 76.6 - - + +
1122A GLY* 1.3 68.6 + - - +
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Residues in contact with GLY1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A GLU 3.0 15.5 + - - -
1119A ALA* 3.3 2.7 + - - -
1120A ILE 3.2 2.1 - - - +
1121A LEU* 1.3 85.0 - - - +
1123A LYS* 1.3 65.2 + - - +
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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