Contacts of the helix formed by residues 1039 - 1052 (chain B) in PDB entry 5V6Y
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 LEU1039 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035B LEU* 2.9 39.7 + - + +
1038B GLU* 1.3 84.1 - - + +
1040B CYS* 1.3 63.9 + - - +
1041B LEU 3.4 0.2 - - - -
1042B THR* 4.4 0.9 - - - -
1043B GLN* 3.9 19.2 + - - +
1072B CYS* 4.4 3.8 - - - -
1076B MET* 3.6 31.4 - - + -
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Residues in contact with CYS1040 (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 LEU 3.7 0.2 + - - -
1036B LEU* 3.1 27.2 + - - +
1039B LEU* 1.3 79.6 - - - +
1041B LEU* 1.3 61.5 + - - +
1042B THR 3.4 0.2 - - - -
1043B GLN* 4.1 2.9 + - - +
1044B PHE* 3.5 12.6 + - - +
1069B LEU* 3.3 26.6 - - + +
1072B CYS* 2.0 66.4 - - + +
1073B THR* 3.6 7.6 - - + -
1076B MET* 4.1 11.2 - - - -
1092B PHE* 4.6 0.9 - - + -
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Residues in contact with LEU1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B LEU 2.8 14.3 + - - +
1037B ARG* 3.3 40.4 + - + +
1039B LEU 3.4 0.2 - - - -
1040B CYS* 1.3 74.3 - - - +
1042B THR* 1.3 59.8 + - - +
1044B PHE* 3.6 17.4 + - + -
1045B GLN* 2.8 34.7 + - + +
1069B LEU* 5.2 0.2 - - + -
1092B PHE* 4.0 9.0 - - + -
1096B VAL* 3.9 27.4 - - + -
1099B ARG* 4.1 28.3 - - - +
1100B TYR* 4.7 11.7 - - + +
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Residues in contact with THR1042 (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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1037B ARG 3.8 5.0 + - - -
1038B GLU* 2.5 29.8 + - - -
1039B LEU 4.0 2.4 + - - -
1040B CYS 3.4 0.4 - - - -
1041B LEU* 1.3 75.8 - - - +
1043B GLN* 1.3 61.2 + - - +
1045B GLN* 3.0 16.6 + - + +
1046B VAL* 2.9 41.2 + - + +
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Residues in contact with GLN1043 (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 3.9 14.0 + - - +
1040B CYS* 4.5 3.1 - - - +
1041B LEU 3.5 0.2 - - - -
1042B THR* 1.3 78.6 - - - +
1044B PHE* 1.3 61.5 + - - +
1046B VAL* 3.4 9.2 + - + +
1047B ASP* 3.1 38.1 + - - +
1068B GLU* 5.5 11.2 + - + +
1072B CYS* 5.2 10.2 - - - +
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Residues in contact with PHE1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040B CYS 3.5 18.0 + - - +
1041B LEU* 3.8 11.2 - - + +
1042B THR 3.2 0.4 - - - -
1043B GLN* 1.3 76.8 - - - +
1045B GLN* 1.3 60.7 + - - +
1047B ASP* 3.3 5.7 + - - +
1048B MET* 3.0 66.8 + - + +
1062B THR 5.4 0.2 - - - -
1065B SER* 3.5 28.3 - - - +
1066B TYR* 4.0 13.7 - + + -
1069B LEU* 3.6 32.3 - - + -
1096B VAL* 3.8 13.0 - - + -
1100B TYR* 3.7 30.5 - + - -
1101B PHE* 4.4 12.8 - + - -
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Residues in contact with GLN1045 (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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1041B LEU* 2.8 26.1 + - + +
1042B THR* 3.0 17.5 + - + +
1044B PHE* 1.3 77.1 - - - +
1046B VAL* 1.3 61.6 + - + +
1048B MET* 4.0 1.4 - - - +
1049B GLU* 3.1 26.3 + - - +
1099B ARG* 5.6 7.6 + - - +
1100B TYR* 3.7 23.6 + - - +
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Residues in contact with VAL1046 (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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1042B THR* 2.9 28.4 + - + +
1043B GLN* 3.7 10.5 - - + +
1044B PHE 3.3 0.4 - - - -
1045B GLN* 1.3 79.5 - - + +
1047B ASP* 1.3 67.1 + - - +
1049B GLU* 3.3 13.7 + - - +
1050B ALA* 3.2 20.6 + - + +
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Residues in contact with ASP1047 (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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1043B GLN* 3.1 27.8 + - - +
1044B PHE* 3.3 4.7 + - - +
1046B VAL* 1.3 84.1 - - - +
1048B MET* 1.3 61.1 + - - +
1050B ALA* 3.1 16.0 + - - +
1051B VAL* 3.3 14.4 + - - +
1065B SER* 3.2 39.1 + - - +
1068B GLU* 4.9 9.9 - - - +
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Residues in contact with MET1048 (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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1044B PHE* 3.0 57.5 + - + +
1045B GLN 4.2 1.8 - - - +
1047B ASP* 1.3 75.5 - - - +
1049B GLU* 1.3 62.4 + - - +
1051B VAL* 3.3 3.8 - - - +
1052B GLY* 3.2 9.2 + - - -
1056B TRP* 2.5 72.3 + - + +
1062B THR* 4.1 23.8 - - + +
1065B SER* 4.5 10.1 - - - -
1100B TYR* 3.6 18.6 - - + -
1101B PHE* 4.2 13.9 - - + -
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Residues in contact with GLU1049 (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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1045B GLN* 3.1 23.1 + - - +
1046B VAL* 3.6 12.4 - - - +
1047B ASP 3.2 0.2 - - - -
1048B MET* 1.3 76.7 - - - +
1050B ALA* 1.3 62.1 + - - +
1052B GLY* 3.8 8.2 + - - +
1053B GLU* 6.4 0.2 - - - -
1056B TRP* 4.3 4.8 - - - -
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Residues in contact with ALA1050 (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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1046B VAL* 3.2 11.5 + - + +
1047B ASP* 3.1 13.4 + - - +
1049B GLU* 1.3 76.4 - - - +
1051B VAL* 1.3 63.4 + - - +
1052B GLY* 3.6 0.3 + - - -
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Residues in contact with VAL1051 (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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1047B ASP 3.3 10.6 + - - +
1048B MET* 3.3 17.3 - - - +
1050B ALA* 1.3 79.1 - - - +
1052B GLY* 1.3 62.8 + - - +
1054B THR* 5.3 0.7 + - - -
1055B LEU* 4.2 24.9 - - + +
1056B TRP* 3.4 18.8 - - + +
1061B ARG* 4.0 41.9 + - + +
1062B THR* 4.3 9.9 - - + -
1065B SER* 6.0 0.9 - - - +
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Residues in contact with GLY1052 (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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1048B MET 3.2 9.9 + - - -
1049B GLU* 3.8 8.0 + - - -
1050B ALA 3.3 2.4 - - - -
1051B VAL* 1.3 79.1 - - - +
1053B GLU* 1.3 64.4 + - - -
1054B THR* 3.1 6.5 - - - -
1055B LEU 3.1 10.8 + - - -
1056B TRP* 2.9 20.9 + - - -
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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