Contacts of the helix formed by residues 1010 - 1020 (chain B) in PDB entry 2ASL
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 TYR1010 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007B ASP* 5.2 0.4 + - - -
1008B PHE 3.5 2.0 + - - -
1009B ASP* 1.3 76.7 - - + +
1011B PHE* 1.3 64.3 + - - +
1012B TYR 3.4 1.6 - - - -
1013B ALA* 3.1 7.3 + - + -
1014B GLN* 3.0 35.3 + - + +
1017B GLU* 3.1 29.9 + - - -
1024B LYS* 5.1 4.2 - - - -
1045B THR* 4.1 10.3 - - - +
1046B ALA 3.4 20.9 - - - +
1047B ASN* 3.2 31.0 - - + -
1048B TYR* 3.2 44.0 + + + -
1049B GLU* 4.8 4.3 + - - -
1051B ARG* 4.2 16.3 - - - +
1139B THR* 5.6 1.8 - - - -
1159B LYS* 6.2 0.2 - - - +
1160B PRO* 6.0 0.9 - - + -
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Residues in contact with PHE1011 (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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1008B PHE* 3.5 38.7 + + + +
1009B ASP 2.7 9.9 + - - -
1010B TYR* 1.3 71.4 - - - +
1012B TYR* 1.3 80.2 + + + +
1014B GLN* 3.1 2.9 + - - +
1015B VAL* 3.1 44.5 + - + +
1045B THR* 4.7 1.0 + - - +
1081B TYR* 3.5 35.9 - - + -
1084B VAL* 4.0 9.4 - - + -
1085B SER* 3.7 17.9 - - - -
1088B ILE* 4.4 4.7 - - + -
1104B ILE* 3.9 23.1 - - + -
1105B ASP* 3.9 16.0 + - + -
1138B ILE* 4.7 9.0 - - + -
1814H DOC 5.8 4.1 - - + -
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Residues in contact with TYR1012 (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 TYR 3.2 1.0 + - - -
1011B PHE* 1.3 86.7 - + + +
1013B ALA* 1.3 63.6 + - - +
1015B VAL 3.4 0.7 + - - -
1016B GLU* 3.3 23.2 + - - +
1030B VAL* 3.9 13.0 - - + -
1044B ALA* 4.4 10.3 - - + -
1045B THR* 3.1 27.6 - - + +
1076B MET* 3.9 17.9 - - - -
1078B LYS* 3.5 28.4 + - + +
1081B TYR* 3.1 57.6 - + + -
1104B ILE* 3.6 26.6 - - + +
1814H DOC 3.8 30.6 + + - -
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Residues in contact with ALA1013 (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 TYR* 3.1 24.2 + - + +
1012B TYR* 1.3 79.2 - - - +
1014B GLN* 1.3 60.8 + - - +
1016B GLU* 3.2 15.8 + - - +
1017B GLU* 3.2 15.8 + - - +
1028B VAL* 4.2 13.9 - - + +
1030B VAL* 3.7 17.6 - - + +
1045B THR* 4.4 3.6 + - - +
1046B ALA* 4.2 4.0 - - - -
1047B ASN* 3.8 22.9 - - + +
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Residues in contact with GLN1014 (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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1009B ASP* 2.9 19.3 - - - +
1010B TYR* 3.0 33.4 + - + +
1011B PHE* 3.1 9.4 + - - +
1013B ALA* 1.3 77.6 - - - +
1015B VAL* 1.3 59.0 + - - +
1017B GLU* 3.2 9.8 + - + +
1018B VAL* 3.1 22.8 + - + +
1137B LYS 3.8 5.9 + - - +
1138B ILE* 3.4 24.2 - - + +
1139B THR* 2.8 59.8 + - - +
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Residues in contact with VAL1015 (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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1011B PHE* 3.1 46.8 + - + +
1012B TYR 3.9 4.3 - - - +
1013B ALA 3.3 0.4 - - - -
1014B GLN* 1.3 72.7 - - - +
1016B GLU* 1.3 64.6 + - - +
1018B VAL* 3.8 8.0 - - + +
1019B LEU* 3.2 36.0 + - + +
1080B VAL* 4.2 7.2 - - + -
1081B TYR* 4.0 22.9 - - + -
1084B VAL* 3.8 30.3 - - + -
1138B ILE* 4.2 6.5 - - + -
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Residues in contact with GLU1016 (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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1012B TYR 3.3 13.9 + - - +
1013B ALA* 3.2 9.7 + - - +
1015B VAL* 1.3 79.3 - - - +
1017B GLU* 1.3 55.9 + - - +
1019B LEU* 3.5 2.9 + - - +
1020B ASN* 2.9 24.6 + - - +
1023B LEU* 3.5 15.5 - - + +
1028B VAL* 4.9 1.6 - - + -
1030B VAL* 4.4 7.2 - - + -
1074B LEU* 3.6 35.8 - - + +
1075B PRO 4.3 4.5 - - - +
1077B ARG* 3.0 40.4 + - - +
1081B TYR* 2.6 29.1 + - + +
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Residues in contact with GLU1017 (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 TYR* 3.1 35.6 + - - -
1013B ALA 3.2 8.0 + - - +
1014B GLN* 3.2 12.8 + - + +
1016B GLU* 1.3 75.7 - - - +
1018B VAL* 1.3 61.5 + - + +
1020B ASN 3.9 5.8 - - - -
1021B PRO* 2.9 33.1 - - + +
1023B LEU* 3.9 21.5 - - + -
1024B LYS* 3.4 42.5 + - + +
1025B GLY 5.4 0.7 - - - -
1028B VAL* 4.6 2.0 - - + +
1047B ASN* 3.3 23.1 + - - -
1049B GLU* 4.9 0.9 - - - +
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Residues in contact with VAL1018 (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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1014B GLN* 3.1 15.8 + - + +
1015B VAL* 3.8 8.7 - - + +
1016B GLU 3.4 0.2 - - - -
1017B GLU* 1.3 77.8 - - + +
1019B LEU* 1.3 69.5 + - + +
1020B ASN 3.6 0.2 + - - -
1021B PRO* 3.8 11.6 - - - +
1136B GLU 3.9 13.5 - - - +
1137B LYS* 3.9 27.1 - - + +
1138B ILE* 3.6 24.0 - - + -
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Residues in contact with LEU1019 (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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1015B VAL* 3.2 31.1 + - + +
1016B GLU* 3.8 4.3 - - - +
1018B VAL* 1.3 91.4 - - + +
1020B ASN* 1.3 59.0 + - + +
1021B PRO* 3.8 3.5 - - - +
1077B ARG* 3.4 35.4 - - - +
1080B VAL* 4.3 17.9 - - + -
1084B VAL* 5.7 3.1 - - + -
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Residues in contact with ASN1020 (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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1016B GLU* 2.9 11.9 + - - +
1017B GLU 3.1 5.2 - - - +
1019B LEU* 1.3 81.4 - - + +
1021B PRO* 1.3 60.8 - - - +
1022B SER* 2.5 38.5 + - - -
1023B LEU* 3.1 35.7 + - + +
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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