Contacts of the helix formed by residues 1040 - 1055 (chain B) in PDB entry 3LW0
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 SER1040 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B ALA 3.7 1.4 + - - -
1039B ALA* 1.3 78.1 - - - +
1041B MET* 1.3 62.0 + - - +
1042B ARG* 3.5 9.1 + - - +
1043B GLU* 2.9 42.8 + - - +
1044B ARG* 3.3 21.3 + - - +
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Residues in contact with MET1041 (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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985B ASP 5.6 4.0 - - - +
1040B SER* 1.3 74.2 - - - +
1042B ARG* 1.3 63.6 + - - +
1044B ARG* 3.3 12.7 + - - +
1045B ILE* 3.3 28.1 + - + +
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Residues in contact with ARG1042 (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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984B ALA 5.7 2.8 + - - -
1040B SER* 3.3 8.3 + - - +
1041B MET* 1.3 81.4 - - - +
1043B GLU* 1.3 58.7 + - + +
1045B ILE* 3.4 7.9 + - + +
1046B GLU* 3.1 46.3 + - + +
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Residues in contact with GLU1043 (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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1010B PHE* 3.6 15.8 - - + -
1035B VAL* 5.3 1.1 - - - -
1039B ALA* 3.7 17.6 - - + +
1040B SER* 2.9 37.8 + - - +
1042B ARG* 1.3 74.8 - - + +
1044B ARG* 1.3 60.6 + - - +
1046B GLU* 3.4 19.2 + - - +
1047B PHE* 3.0 29.5 + - - +
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Residues in contact with ARG1044 (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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987B TYR* 5.0 7.9 + - - +
1035B VAL* 4.6 12.9 - - + +
1040B SER 3.3 10.1 + - - +
1041B MET* 3.3 15.7 + - - +
1043B GLU* 1.3 78.3 - - - +
1045B ILE* 1.3 82.1 + - - +
1047B PHE* 3.4 7.3 - - - +
1048B LEU* 3.0 47.9 + - + +
1070B SER* 3.0 29.9 + - - -
1071B GLN* 5.3 1.2 - - - +
1072B GLY 5.5 2.2 + - - -
1073B GLN* 5.5 4.9 - - - +
1075B THR* 3.6 29.2 + - + +
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Residues in contact with ILE1045 (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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983B ALA 3.8 11.7 - - - +
984B ALA 3.9 16.2 - - - +
985B ASP 3.6 24.0 - - - +
986B VAL* 4.0 3.1 - - - +
987B TYR* 3.9 22.4 - - + +
1041B MET* 3.3 20.3 + - + +
1042B ARG* 3.7 9.9 - - + +
1043B GLU 3.2 0.4 - - - -
1044B ARG* 1.3 101.0 - - - +
1046B GLU* 1.3 55.4 + - + +
1048B LEU* 3.1 4.0 + - - +
1049B ASN* 2.7 55.6 + - - +
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Residues in contact with GLU1046 (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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1010B PHE* 4.0 18.3 - - + -
1042B ARG* 3.1 46.1 + - + +
1043B GLU* 3.6 20.6 - - - +
1045B ILE* 1.3 73.0 - - + +
1047B PHE* 1.3 62.5 - - - +
1049B ASN* 3.3 9.5 + - - +
1050B GLU* 3.0 28.1 + - + +
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Residues in contact with PHE1047 (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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2B CCX 4.9 1.6 + - - -
1010B PHE* 3.5 40.5 - + + -
1033B LYS* 3.8 47.7 + - + -
1034B THR 3.9 15.9 - - - -
1035B VAL* 3.2 26.5 - - + -
1043B GLU 3.0 17.3 + - - +
1044B ARG 3.4 3.6 - - - +
1046B GLU* 1.3 76.9 - - - +
1048B LEU* 1.3 64.0 + - + +
1050B GLU* 3.3 13.8 + - - +
1051B ALA* 3.4 10.7 + - - +
1075B THR* 3.9 21.1 - - + -
1076B LEU 4.1 3.1 - - - -
1077B VAL* 3.5 29.3 - - + +
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Residues in contact with LEU1048 (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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987B TYR* 3.8 35.9 - - + -
1044B ARG* 3.0 59.4 + - + +
1045B ILE* 3.6 4.0 - - - +
1047B PHE* 1.3 84.8 - - + +
1049B ASN* 1.3 56.9 + - - +
1051B ALA* 3.1 7.7 + - - +
1052B SER* 2.9 30.6 + - - -
1068B VAL* 3.7 30.1 - - + -
1070B SER* 4.3 3.8 - - - -
1075B THR* 3.8 22.0 - - + -
1077B VAL* 4.6 3.6 - - + -
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Residues in contact with ASN1049 (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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983B ALA* 3.2 32.9 + - - +
984B ALA* 4.8 3.2 - - - +
986B VAL 5.0 3.1 - - - +
987B TYR* 5.2 4.7 - - - +
1045B ILE* 2.7 36.7 + - - +
1046B GLU* 3.8 8.4 - - - +
1048B LEU* 1.3 69.7 - - - +
1050B GLU* 1.3 66.2 + - - +
1052B SER* 3.2 13.3 + - - -
1053B VAL* 3.1 30.4 + - + +
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Residues in contact with GLU1050 (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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2B CCX 3.8 46.5 + - + +
1009B SER* 5.2 0.9 + - - -
1010B PHE* 3.4 36.2 - - - -
1033B LYS* 3.9 14.7 + - - -
1046B GLU* 3.0 15.1 + - + +
1047B PHE 3.4 8.6 - - - +
1048B LEU 3.2 0.4 - - - -
1049B ASN* 1.3 75.4 - - - +
1051B ALA* 1.3 59.1 + - - +
1053B VAL* 3.0 25.4 - - - +
1054B MET* 3.4 11.6 - - - +
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Residues in contact with ALA1051 (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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2B CCX 3.5 14.3 + - - +
987B TYR* 5.8 0.2 - - + -
1047B PHE 3.4 3.5 + - - +
1048B LEU* 3.1 11.3 + - + +
1050B GLU* 1.3 78.7 - - - +
1052B SER* 1.3 63.7 + - - +
1054B MET* 3.0 12.1 + - - -
1055B LYS* 3.4 8.9 + - - -
1065B LEU* 3.5 24.7 - - + +
1068B VAL* 4.3 11.9 - - + -
1077B VAL* 3.8 28.9 - - + -
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Residues in contact with SER1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987B TYR* 3.3 24.3 - - - -
1048B LEU 2.9 17.3 + - - -
1049B ASN* 3.2 17.3 + - - -
1051B ALA* 1.3 76.7 - - - +
1053B VAL* 1.3 62.9 + - - +
1054B MET 3.3 1.0 + - - -
1055B LYS* 3.3 32.7 + - - +
1056B GLU* 4.7 0.9 + - - +
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Residues in contact with VAL1053 (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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2B CCX 6.4 1.3 - - - -
1049B ASN* 3.1 15.0 + - + +
1050B GLU* 3.0 29.8 - - - +
1052B SER* 1.3 76.5 - - - +
1054B MET* 1.3 72.1 + - - +
1056B GLU* 3.5 24.4 - - - +
1057B PHE* 3.6 8.1 - - - -
1131B PHE* 4.6 15.5 - - + -
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Residues in contact with MET1054 (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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2B CCX 3.6 71.3 - - + +
992B TRP* 5.5 0.7 - - - -
1050B GLU 3.4 15.7 - - - +
1051B ALA 3.0 8.0 + - - +
1053B VAL* 1.3 85.2 - - - +
1055B LYS* 1.3 64.2 + - - +
1056B GLU 3.1 3.1 - - - -
1057B PHE* 3.1 53.6 + - + +
1062B VAL* 4.2 11.2 - - + -
1063B VAL 5.1 0.4 - - - +
1065B LEU* 4.4 13.4 + - + +
1126B LEU* 4.7 5.4 - - + -
1131B PHE* 4.2 12.3 - - + -
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Residues in contact with LYS1055 (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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987B TYR* 2.9 36.8 + - - -
988B VAL 4.9 1.0 + - - -
990B ASP* 2.8 25.2 + - - +
992B TRP* 3.4 57.0 - - + +
1051B ALA 3.4 2.8 + - - +
1052B SER* 3.3 31.6 + - - +
1054B MET* 1.3 77.4 - - - +
1056B GLU* 1.3 60.0 - - - +
1057B PHE 3.5 3.6 + - - +
1065B LEU* 3.5 20.9 - - + -
1068B VAL* 4.7 3.4 - - - -
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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