Contacts of the helix formed by residues 1036 - 1054 (chain A) in PDB entry 6AH0
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 PHE1036 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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919A ASP 5.1 13.1 + - - -
920A ALA* 5.5 1.0 - - - +
923A ASP* 5.2 11.4 - - - +
1034A LEU* 3.1 0.6 - - - +
1035A GLN* 1.3 75.1 - - - +
1037A ALA* 1.3 64.4 + - - +
1038A SER 3.2 2.9 - - - +
1039A PHE* 3.3 13.6 + - - +
1040A ILE* 3.3 8.8 + - - -
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Residues in contact with ALA1037 (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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1031A ILE 4.7 9.4 - - - -
1032A ARG* 4.6 10.5 - - - +
1034A LEU* 3.1 16.7 + - - +
1036A PHE* 1.3 78.8 - - - +
1038A SER* 1.3 56.8 + - - +
1040A ILE* 3.1 3.6 + - - +
1041A VAL* 2.9 26.3 + - - -
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Residues in contact with SER1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A ARG 5.4 0.8 + - - -
1034A LEU 4.7 1.2 + - - -
1035A GLN 4.8 2.6 + - - -
1036A PHE* 3.2 1.2 - - - +
1037A ALA* 1.3 76.1 - - - +
1039A PHE* 1.3 55.7 + - - +
1041A VAL* 3.2 2.0 + - - +
1042A GLN* 2.9 26.7 + - - -
1438A VAL* 5.8 9.6 - - - +
1439A ARG* 5.9 3.4 - - - +
1442A PHE* 6.2 3.6 - - - +
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Residues in contact with PHE1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A PHE* 3.3 9.3 + - - +
1037A ALA 3.2 0.8 - - - -
1038A SER* 1.3 75.6 - - - +
1040A ILE* 1.3 62.9 + - - +
1042A GLN* 3.4 1.8 + - - +
1043A TYR* 3.0 19.9 + - - -
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Residues in contact with ILE1040 (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 PHE 3.3 7.9 + - - -
1037A ALA* 3.1 7.4 + - - +
1039A PHE* 1.3 75.0 - - - +
1041A VAL* 1.3 58.7 + - - +
1043A TYR* 3.2 1.9 + - - +
1044A TYR* 2.9 28.1 + - - -
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Residues in contact with VAL1041 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A ALA 2.9 13.9 + - - -
1038A SER* 3.2 3.6 + - - +
1040A ILE* 1.3 77.3 - - - +
1042A GLN* 1.3 55.6 + - - +
1044A TYR* 4.0 0.8 - - - +
1045A GLY* 2.9 27.2 + - - -
1092A ILE* 4.5 6.6 - - - +
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Residues in contact with GLN1042 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A SER 2.9 15.4 + - - -
1039A PHE* 3.9 1.8 - - - +
1040A ILE 3.3 0.2 - - - -
1041A VAL* 1.3 78.6 - - - +
1043A TYR* 1.3 61.1 + - - +
1045A GLY* 3.8 0.5 - - - -
1046A LEU* 3.0 20.6 + - - -
1092A ILE* 4.6 19.6 - - - +
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Residues in contact with TYR1043 (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 PHE 3.0 14.4 + - - -
1040A ILE* 3.7 3.1 - - - +
1042A GLN* 1.3 77.2 - - - +
1044A TYR* 1.3 62.1 + - - +
1046A LEU* 3.2 11.8 + - - +
1047A VAL* 3.2 9.0 + - - -
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Residues in contact with TYR1044 (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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1040A ILE 2.9 15.9 + - - -
1041A VAL* 4.0 0.7 - - - +
1043A TYR* 1.3 75.4 - - - +
1045A GLY* 1.3 62.9 + - - +
1047A VAL* 3.1 12.0 + - - +
1048A MET* 3.2 9.0 + - - -
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Residues in contact with GLY1045 (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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1041A VAL 2.9 18.0 + - - -
1042A GLN 3.8 1.8 - - - -
1044A TYR* 1.3 75.3 - - - +
1046A LEU* 1.3 50.0 + - - +
1048A MET* 2.9 6.5 + - - -
1049A ASP* 2.8 31.0 + - - -
1092A ILE 4.2 14.1 - - - -
1093A ASP* 5.6 3.1 - - - -
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Residues in contact with LEU1046 (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 GLN 3.0 15.5 + - - -
1043A TYR* 3.2 5.6 + - - +
1045A GLY* 1.3 74.1 - - - +
1047A VAL* 1.3 62.8 + - - +
1049A ASP* 3.1 12.6 + - - +
1050A LEU* 3.1 9.7 + - - -
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Residues in contact with VAL1047 (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 TYR 3.2 7.3 + - - -
1044A TYR* 3.1 9.9 + - - +
1046A LEU* 1.3 75.2 - - - +
1048A MET* 1.3 62.5 + - - +
1050A LEU* 3.2 11.3 + - - -
1051A LEU* 3.3 8.8 + - - -
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Residues in contact with MET1048 (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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1044A TYR 3.2 7.4 + - - -
1045A GLY* 2.9 8.7 + - - -
1047A VAL* 1.3 74.3 - - - +
1049A ASP* 1.3 59.7 + - - +
1051A LEU* 3.1 3.8 + - - +
1052A VAL* 2.9 25.3 + - - -
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Residues in contact with ASP1049 (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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1045A GLY 2.8 12.7 + - - -
1046A LEU* 3.1 7.0 + - - +
1048A MET* 1.3 75.7 - - - +
1050A LEU* 1.3 53.3 + - - +
1052A VAL* 3.3 1.1 + - - +
1053A LEU* 2.6 36.3 + - - +
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Residues in contact with LEU1050 (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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1046A LEU 3.1 12.5 + - - -
1047A VAL* 3.2 5.8 + - - +
1049A ASP* 1.3 76.1 - - - +
1051A LEU* 1.3 62.6 + - - +
1054A GLY* 3.5 20.3 + - - +
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Residues in contact with LEU1051 (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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1047A VAL 3.3 9.1 + - - -
1048A MET* 3.1 8.2 + - - +
1050A LEU* 1.3 78.7 - - - +
1052A VAL* 1.3 59.8 + - - +
1054A GLY* 4.8 1.4 + - - -
1160A ARG* 3.9 14.8 - - - +
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Residues in contact with VAL1052 (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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1048A MET 2.9 13.4 + - - -
1049A ASP* 3.7 1.8 - - - +
1051A LEU* 1.3 77.8 - - - +
1053A LEU* 1.3 62.5 + - - +
1054A GLY* 3.7 0.3 + - - -
1160A ARG* 5.0 9.6 - - - +
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Residues in contact with LEU1053 (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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1049A ASP 2.6 21.6 + - - -
1052A VAL* 1.3 74.7 - - - +
1054A GLY* 1.3 64.2 + - - +
1057A ARG* 5.1 3.1 + - - -
1058A ALA* 4.6 8.6 + - - +
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Residues in contact with GLY1054 (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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1050A LEU* 3.5 17.6 + - - +
1051A LEU 4.8 1.5 + - - -
1052A VAL 3.6 2.0 - - - -
1053A LEU* 1.3 75.3 - - - +
1055A LEU* 1.3 59.8 + - - -
1056A HIS 3.5 2.2 - - - -
1057A ARG 4.6 0.7 - - - -
1058A ALA* 3.1 27.6 + - - -
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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