Contacts of the helix formed by residues 1131 - 1142 (chain B) in PDB entry 1Y1V
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 GLY1131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A MET 4.2 2.2 - - - -
342A GLY* 4.0 1.8 - - - -
1129B ARG* 3.5 24.8 - - - +
1130B PHE* 1.3 77.1 - - - +
1132B GLU* 1.3 71.3 + - - +
1133B MET 3.1 1.3 - - - -
1134B GLU* 2.6 37.8 + - - +
1135B ARG* 2.8 7.9 + - - -
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Residues in contact with GLU1132 (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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332A LYS* 5.4 1.6 + - - +
337A ARG* 2.8 50.7 + - + +
341A MET* 3.8 33.3 + - + +
342A GLY* 4.3 1.4 - - - +
839A ARG* 3.8 24.5 + - - -
843A LYS* 4.5 11.3 + - - +
1401A SER 4.9 0.2 - - - +
1129B ARG* 5.2 3.5 - - - +
1131B GLY* 1.3 68.0 - - - -
1133B MET* 1.3 55.8 + - + +
1135B ARG* 2.5 31.1 + - - +
1136B ASP* 2.7 29.2 + - - +
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Residues in contact with MET1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PRO* 4.1 20.0 - - + -
449A SER* 3.1 44.6 - - - +
450A LEU* 4.3 16.8 - - + -
838A GLN* 4.5 15.0 - - + +
1070A GLN* 4.9 0.2 + - - -
1131B GLY 2.9 3.4 + - - -
1132B GLU* 1.3 79.9 - - + +
1134B GLU* 1.3 72.4 + - - +
1136B ASP* 3.4 11.9 + - - +
1137B CYS* 3.0 24.3 + - - +
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Residues in contact with GLU1134 (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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445A ASN* 4.3 3.1 - - - +
447A GLN* 3.1 30.3 + - - +
449A SER* 3.2 18.7 + - - +
455A MET* 3.1 39.7 - - + +
488A ASN* 5.8 1.3 - - - +
490A HIS* 5.3 1.3 - - - +
1129B ARG 4.7 2.7 - - - +
1130B PHE* 3.5 35.1 - - + -
1131B GLY* 2.6 49.7 + - - +
1133B MET* 1.3 80.0 + - - +
1135B ARG* 1.3 60.3 + - - +
1137B CYS* 3.7 3.8 - - - +
1138B MET* 3.4 11.8 + - - +
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Residues in contact with ARG1135 (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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341A MET* 2.9 48.9 - - - +
842A VAL* 5.0 1.4 - - - +
843A LYS* 3.5 12.9 - - - +
846A GLU* 3.1 31.3 + - - +
1066A VAL* 6.1 0.4 - - - +
1424A VAL* 4.0 8.1 - - - +
1425A SER* 3.3 4.0 + - - +
1428A VAL* 4.3 15.0 - - + +
1130B PHE* 4.5 11.0 - - + -
1131B GLY 2.8 5.9 + - - +
1132B GLU* 2.5 30.1 + - - +
1134B GLU* 1.3 68.6 - - - +
1136B ASP* 1.3 93.3 + - - -
1137B CYS 2.9 1.1 - - - -
1138B MET* 2.7 18.0 + - - +
1139B ILE* 3.0 35.3 + - + +
1147B LEU* 4.1 15.5 - - + -
1151B LEU* 5.8 2.9 - - + -
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Residues in contact with ASP1136 (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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838A GLN* 5.5 1.4 - - - +
839A ARG* 6.1 0.2 - - - -
842A VAL* 3.3 31.9 - - + +
1066A VAL* 3.5 9.7 - - + +
1070A GLN* 4.3 11.0 - - - +
1132B GLU* 2.7 26.8 + - - +
1133B MET* 3.8 11.9 + - - +
1135B ARG* 1.3 110.6 + - - +
1137B CYS* 1.3 57.2 + - - +
1139B ILE* 3.2 12.3 + - - +
1140B ALA* 2.8 28.2 + - - +
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Residues in contact with CYS1137 (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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449A SER* 4.1 14.4 - - - -
451A HIS 2.7 40.6 - - - -
452A LYS* 4.2 2.5 - - - -
455A MET* 4.1 19.5 - - + -
1070A GLN* 3.8 11.4 - - - +
1133B MET 3.0 17.5 + - - +
1134B GLU 3.7 7.9 - - - +
1135B ARG 2.9 1.0 + - - -
1136B ASP* 1.3 78.0 - - - +
1138B MET* 1.3 61.3 + - - +
1140B ALA* 3.2 8.9 - - - +
1141B HIS* 3.1 26.9 + - + -
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Residues in contact with MET1138 (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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443A LEU* 4.2 13.0 - - + -
455A MET* 4.0 28.5 - - + +
505A CYS* 3.6 32.8 - - + -
1130B PHE* 4.4 10.3 - - + -
1134B GLU 3.4 7.8 + - - +
1135B ARG* 2.7 14.3 + - - +
1137B CYS* 1.3 71.5 - - - +
1139B ILE* 1.3 56.5 + - - +
1141B HIS* 2.6 46.6 + - + +
1142B GLY 2.8 11.4 + - - -
1143B ALA* 3.6 20.9 + - + +
1146B PHE* 4.1 23.3 - - + -
1147B LEU* 4.1 23.1 - - + -
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Residues in contact with ILE1139 (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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846A GLU* 5.4 1.8 - - + +
1063A MET* 2.9 38.1 - - + +
1066A VAL* 4.4 15.5 - - + -
1424A VAL* 3.6 17.9 - - + -
1436A ILE* 3.3 36.8 - - + -
1135B ARG* 3.0 57.4 - - + +
1136B ASP* 3.4 10.8 - - - +
1138B MET* 1.3 73.2 - - - +
1140B ALA* 1.3 63.7 + - - +
1142B GLY* 3.2 6.6 + - - +
1143B ALA 5.4 0.7 - - - +
1147B LEU* 4.2 9.6 - - + +
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Residues in contact with ALA1140 (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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452A LYS* 3.7 27.6 + - + +
1062A GLU* 5.2 3.5 - - - +
1063A MET* 4.5 16.3 + - - +
1066A VAL* 3.9 20.8 - - + +
1067A LEU* 4.8 8.6 - - - +
1070A GLN* 4.2 8.3 - - - +
1136B ASP 2.8 14.0 + - - +
1137B CYS* 3.2 14.6 - - - +
1139B ILE* 1.3 78.3 - - - +
1141B HIS* 1.3 61.2 + - - +
1142B GLY* 3.5 0.5 + - - -
88F TYR* 4.7 3.5 + - - -
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Residues in contact with HIS1141 (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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452A LYS* 2.8 44.1 + - + +
455A MET* 3.2 12.8 + - + -
504A LEU* 4.1 11.2 + - - +
505A CYS* 3.8 31.2 - - - -
510A GLN* 3.4 37.5 + - + -
1137B CYS 3.1 21.7 + - - -
1138B MET* 2.6 34.8 + - + +
1140B ALA* 1.3 72.9 - - - +
1142B GLY* 1.3 54.8 + - - +
1143B ALA 3.3 4.6 + - - +
88F TYR* 3.3 20.4 + - - -
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Residues in contact with GLY1142 (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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504A LEU* 4.3 2.0 - - - -
1063A MET* 4.8 1.6 - - - -
1436A ILE* 3.3 17.1 - - - +
1438A THR* 3.2 23.9 + - - -
1138B MET 2.8 5.2 + - - -
1139B ILE 3.2 12.4 + - - -
1140B ALA 4.5 0.7 - - - -
1141B HIS* 1.3 78.1 - - - +
1143B ALA* 1.3 50.1 - - - +
1144B ALA 2.5 20.2 + - - -
88F TYR* 3.4 17.9 - - - -
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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