Contacts of the helix formed by residues 1036 - 1043 (chain B) in PDB entry 3SQD
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 CYS1036 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979B TYR* 6.4 0.7 - - - -
981B THR* 4.0 14.1 - - - -
1026B LEU* 6.1 2.7 - - - -
1027B ILE 5.5 0.4 - - - -
1028B SER* 3.7 33.7 - - - -
1032B ASP 4.2 1.1 - - - -
1033B LEU* 3.1 4.2 + - - +
1034B HIS 3.0 1.2 - - - -
1035B LEU* 1.3 80.0 - - - +
1037B ARG* 1.3 64.1 + - - +
1038B GLU 3.2 3.1 - - - -
1039B TYR* 2.8 34.4 + - + +
1040B PHE* 3.1 33.7 + - + -
1046B VAL* 4.4 9.9 - - + -
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Residues in contact with ARG1037 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010A ARG* 3.4 26.9 - - - +
1014A GLU* 3.1 37.7 + - - +
1018A ASN* 3.8 27.2 + - - +
1021A LEU* 4.0 15.5 - - + -
1033B LEU 3.6 2.8 + - - -
1034B HIS 3.0 13.5 + - - +
1035B LEU 3.4 1.0 + - - -
1036B CYS* 1.3 77.7 - - - +
1038B GLU* 1.3 96.7 + - + +
1040B PHE* 3.3 11.8 + - - +
1041B ALA* 2.8 28.9 + - - +
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Residues in contact with GLU1038 (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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1018A ASN* 5.7 0.2 - - - +
1006B GLN* 5.4 6.8 + - - +
1009B PHE* 3.4 26.3 - - + -
1035B LEU 4.6 9.0 - - - +
1036B CYS 3.0 1.4 + - - -
1037B ARG* 1.3 123.9 + - + +
1039B TYR* 1.3 67.5 + - + +
1041B ALA* 3.4 8.2 + - - +
1042B ARG* 3.1 16.6 + - - +
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Residues in contact with TYR1039 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979B TYR* 5.9 2.5 - + - -
1006B GLN* 3.3 42.4 + - + +
1007B PRO* 2.6 31.2 + - + +
1008B SER 5.3 0.2 - - - -
1009B PHE* 3.7 21.5 - + - -
1012B LEU* 3.4 34.1 - - + -
1026B LEU* 3.8 27.6 - - + -
1035B LEU 4.7 2.0 - - - -
1036B CYS* 2.8 30.9 + - + +
1038B GLU* 1.3 80.5 - - + +
1040B PHE* 1.3 65.4 + - - +
1042B ARG 3.2 1.9 + - - -
1043B GLY 3.0 5.0 + - - -
1044B ILE* 2.9 34.7 + - + +
1046B VAL* 4.6 5.8 - - + -
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Residues in contact with PHE1040 (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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1020A SER* 3.1 40.5 + - - +
1021A LEU* 3.9 14.1 - - + -
1033B LEU* 3.7 33.2 - - + -
1036B CYS* 3.1 48.9 + - + -
1037B ARG* 3.4 6.7 - - - +
1039B TYR* 1.3 77.3 - - - +
1041B ALA* 1.3 63.4 + - - +
1043B GLY* 3.0 14.0 + - - -
1046B VAL* 3.7 20.4 - - + -
1068B PHE* 3.8 22.4 - - + -
1069B ASN* 3.8 33.7 + - + +
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Residues in contact with ALA1041 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A ASN* 4.1 15.0 - - - +
1020A SER* 3.8 6.2 + - - -
1037B ARG 2.8 16.8 + - - +
1038B GLU* 3.7 10.1 - - + +
1039B TYR 3.3 0.4 - - - -
1040B PHE* 1.3 76.7 - - - +
1042B ARG* 1.3 59.8 + - - +
1043B GLY 3.5 0.2 + - - -
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Residues in contact with ARG1042 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009B PHE* 3.7 58.0 - - + +
1013B MET* 6.0 3.6 - - - +
1038B GLU 3.1 15.5 + - - +
1039B TYR 3.2 2.4 + - - +
1040B PHE 3.1 1.0 - - - -
1041B ALA* 1.3 77.6 - - - +
1043B GLY* 1.3 58.5 + - - +
1044B ILE* 3.6 8.0 - - + +
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Residues in contact with GLY1043 (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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1040B PHE 3.0 15.3 + - - -
1041B ALA 3.3 0.6 - - - -
1042B ARG* 1.3 80.0 - - - +
1044B ILE* 1.3 63.3 + - - +
1045B ASP* 3.7 4.7 + - - +
1069B ASN* 4.4 5.9 + - - -
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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