Contacts of the helix formed by residues 1035 - 1048 (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 ALA1035 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033A GLU 4.3 0.8 + - - -
1034A TYR* 1.3 73.4 - - - +
1036A LEU* 1.3 65.4 + - - +
1037A PRO 3.3 0.2 - - - -
1038A VAL* 3.0 5.9 + - - +
1039A LEU* 2.8 25.3 + - + +
1111A PHE* 4.0 16.8 - - + -
1114A ASP* 3.7 22.5 + - - +
1115A ALA* 3.7 30.3 - - + -
1118A GLU* 4.1 14.8 + - + +
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Residues in contact with LEU1036 (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* 4.4 4.2 - - + +
1035A ALA* 1.3 76.9 - - - +
1037A PRO* 1.3 72.8 - - + +
1039A LEU* 3.1 16.6 + - + +
1040A THR* 3.0 31.5 + - - +
1043A ARG* 5.9 2.2 - - - +
1118A GLU* 3.9 11.6 + - - +
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Residues in contact with PRO1037 (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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988A CYS* 3.6 27.3 - - + +
989A TYR* 5.5 1.4 - - - -
1023A TYR* 3.6 20.9 - - - +
1034A TYR* 3.3 28.0 - - + +
1035A ALA 3.4 0.4 - - - -
1036A LEU* 1.3 98.6 - - + +
1038A VAL* 1.3 56.2 + - - +
1040A THR* 3.5 8.2 + - - +
1041A PHE* 3.0 26.2 + - - +
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Residues in contact with VAL1038 (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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1023A TYR* 3.6 26.7 - - + +
1026A TRP* 4.7 10.1 - - + -
1032A PRO* 4.1 17.3 - - + -
1034A TYR 4.5 2.9 - - - +
1035A ALA* 3.0 8.2 + - + +
1037A PRO* 1.3 77.1 - - - +
1039A LEU* 1.3 56.1 + - + +
1041A PHE* 3.1 10.4 + - + +
1042A VAL* 2.7 51.8 + - + +
1069A THR* 6.3 0.2 - - + -
1073A ILE* 4.7 7.9 - - + -
1111A PHE* 4.0 33.7 - - + -
1115A ALA* 6.0 0.7 - - + -
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Residues in contact with LEU1039 (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 2.8 20.3 + - - +
1036A LEU* 3.5 16.6 - - + +
1038A VAL* 1.3 77.9 - - + +
1040A THR* 1.3 56.1 + - - +
1042A VAL* 3.8 3.4 - - - +
1043A ARG* 3.0 61.5 + - - +
1073A ILE* 4.2 24.2 - - + -
1077A LEU* 4.4 9.2 - - + -
1115A ALA* 3.5 36.6 - - + +
1118A GLU* 4.1 12.3 - - + -
1119A ALA* 3.9 19.7 - - + +
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Residues in contact with THR1040 (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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989A TYR* 4.7 6.5 - - + -
1036A LEU* 3.0 22.1 + - - +
1037A PRO* 3.6 11.1 - - - +
1039A LEU* 1.3 75.0 - - - +
1041A PHE* 1.3 65.8 + - - +
1043A ARG* 4.0 5.7 - - - +
1044A ARG* 3.1 65.7 + - - +
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Residues in contact with PHE1041 (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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948A VAL* 3.8 21.3 - - + -
949A MET 4.4 0.7 - - - -
950A ILE* 4.7 6.5 - - + -
989A TYR* 3.6 39.5 - + + -
1021A TYR* 3.4 45.3 - + + -
1022A HIS 3.9 0.2 - - - -
1023A TYR* 3.6 47.6 - + + -
1037A PRO 3.0 15.1 + - - +
1038A VAL* 3.4 11.0 - - + +
1040A THR* 1.3 79.2 - - - +
1042A VAL* 1.3 54.1 + - + +
1044A ARG* 4.2 1.9 - - - +
1045A SER* 2.6 40.7 + - - -
1070A TYR* 4.1 13.7 - + - -
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Residues in contact with VAL1042 (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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1038A VAL* 2.7 37.2 + - + +
1039A LEU* 3.8 6.5 - - - +
1041A PHE* 1.3 71.7 - - + +
1043A ARG* 1.3 65.7 + - - +
1045A SER* 3.3 5.3 + - - -
1046A SER* 2.9 27.4 + - - -
1070A TYR* 3.9 24.7 + - + -
1073A ILE* 4.2 17.5 - - + -
1074A ASP* 4.0 27.8 - - + +
1077A LEU* 3.7 25.1 - - + -
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Residues in contact with ARG1043 (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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1036A LEU* 5.9 2.4 - - - +
1039A LEU* 3.0 45.3 + - - +
1040A THR* 4.0 5.9 - - - +
1042A VAL* 1.3 76.1 - - - +
1044A ARG* 1.3 60.3 + - + +
1046A SER* 3.6 5.2 - - - -
1047A ALA* 3.1 30.1 + - - +
1077A LEU* 4.2 23.3 - - + +
1119A ALA* 3.6 38.2 + - - +
1123A LYS* 6.3 1.2 - - - +
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Residues in contact with ARG1044 (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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986A HIS* 4.4 13.1 + - - -
989A TYR* 2.9 32.7 + - + +
1021A TYR* 4.0 14.1 + - + +
1040A THR* 3.1 43.7 + - + +
1041A PHE* 4.2 2.0 - - - +
1043A ARG* 1.3 76.4 - - + +
1045A SER* 1.3 66.6 + - - +
1047A ALA* 3.5 6.2 + - - +
1048A ALA* 3.2 22.0 + - - +
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Residues in contact with SER1045 (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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946A ILE* 4.1 12.6 - - - +
948A VAL* 4.4 7.6 - - - +
1021A TYR* 3.5 39.4 - - - -
1041A PHE* 2.6 26.7 + - - -
1042A VAL 3.3 2.6 + - - -
1044A ARG* 1.3 76.7 - - - +
1046A SER* 1.3 60.1 + - - +
1048A ALA* 3.8 11.4 + - - +
1049A ARG* 4.2 2.6 + - - +
1056A VAL* 5.5 2.4 - - - +
1070A TYR* 2.8 31.4 + - - -
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Residues in contact with SER1046 (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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1042A VAL 2.9 20.1 + - - -
1043A ARG* 3.6 6.3 - - - -
1045A SER* 1.3 75.0 + - - +
1047A ALA* 1.3 65.3 + - - +
1048A ALA 3.1 1.8 - - - -
1049A ARG* 3.1 29.1 + - - +
1070A TYR* 4.3 3.6 - - - -
1074A ASP* 2.6 35.8 + - - -
1078A GLN* 4.6 10.0 + - - +
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Residues in contact with ALA1047 (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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1043A ARG 3.1 18.1 + - - +
1044A ARG* 4.0 5.8 - - - +
1046A SER* 1.3 71.9 - - - +
1048A ALA* 1.3 60.3 + - - +
1049A ARG 3.0 13.4 + - - +
1050A MET* 4.5 9.5 - - - +
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Residues in contact with ALA1048 (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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946A ILE* 3.6 30.3 - - + +
1019A ILE* 5.7 3.1 - - + -
1021A TYR* 3.6 31.0 - - + +
1044A ARG 3.2 9.2 + - - +
1045A SER 3.8 4.3 - - - +
1046A SER 3.1 0.8 - - - -
1047A ALA* 1.3 75.8 - - - +
1049A ARG* 1.3 57.4 + - - +
1050A MET* 3.0 27.5 + - - +
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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