Contacts of the helix formed by residues 1002 - 1019 (chain B) in PDB entry YUA9
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 ASN1002 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952B GLY* 3.8 12.7 - - - +
953B THR* 2.9 32.4 + - + +
1000B VAL* 5.2 2.2 - - + -
1001B CYS* 1.3 76.7 - - - +
1003B LYS* 1.3 60.9 + - - +
1004B LYS* 3.0 31.2 + - - +
1005B LEU* 3.2 34.8 + - + +
1006B TRP* 3.0 29.8 + - - +
1040B ILE 5.1 0.4 - - - +
1041B HIS 3.9 4.2 + - - -
1148B TYR* 2.9 11.8 + - + +
1164B PEG 3.8 4.9 + - - -
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Residues in contact with LYS1003 (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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952B GLY 4.9 1.4 + - - -
1002B ASN* 1.3 73.4 + - - +
1004B LYS* 1.3 59.0 + - - +
1006B TRP* 3.2 7.0 + - + +
1007B GLU* 2.9 65.6 + - + +
1164B PEG 3.8 14.6 + - - +
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Residues in contact with LYS1004 (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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952B GLY* 3.9 24.4 - - - +
1002B ASN* 3.0 21.4 + - - +
1003B LYS* 1.3 78.6 - - - +
1005B LEU* 1.3 72.8 - - + +
1007B GLU* 3.3 11.2 + - - +
1008B ARG* 2.9 36.6 + - + +
1041B HIS 4.5 7.9 + - - -
1042B LYS* 5.9 1.1 - - - +
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Residues in contact with LEU1005 (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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1000B VAL* 6.2 0.7 - - + -
1002B ASN* 3.2 39.7 + - + +
1004B LYS* 1.3 88.8 - - - +
1006B TRP* 1.3 61.4 + - - +
1008B ARG* 3.5 28.2 + - - +
1009B TYR* 3.1 22.0 + - - +
1039B ILE 4.6 0.4 - - - +
1040B ILE 4.1 9.6 - - - +
1041B HIS 4.0 6.3 - - - +
1042B LYS 3.4 22.9 - - - +
1043B GLY* 3.7 26.9 - - - +
1147B ALA 5.5 0.7 - - - +
1148B TYR* 3.8 17.1 - - + -
1149B PRO* 5.6 5.6 - - + -
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Residues in contact with TRP1006 (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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1002B ASN 3.0 17.8 + - - +
1003B LYS* 3.4 8.1 - - + +
1004B LYS 3.1 0.2 - - - -
1005B LEU* 1.3 77.2 - - - +
1007B GLU* 1.3 66.1 - - + +
1009B TYR* 2.9 22.4 + + - +
1010B THR* 2.9 53.8 + - + +
1013B ARG* 4.5 8.3 - - - -
1100B ARG* 4.0 20.6 - - - -
1148B TYR* 3.7 29.6 - + + -
1150B GLU* 3.6 13.5 - - - -
1164B PEG 3.5 41.9 - - - -
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Residues in contact with GLU1007 (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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1003B LYS* 2.9 60.5 + - + +
1004B LYS* 3.3 8.7 + - - +
1006B TRP* 1.3 79.3 - - + +
1008B ARG* 1.3 64.6 + - - +
1010B THR* 3.5 9.5 + - - +
1011B HIS* 3.1 27.0 + - - +
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Residues in contact with ARG1008 (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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1004B LYS* 2.9 20.7 + - + +
1005B LEU* 3.5 28.2 + - - +
1007B GLU* 1.3 76.1 - - - +
1009B TYR* 1.3 62.9 + - - +
1011B HIS* 3.8 3.9 + - - +
1012B ARG* 3.2 23.9 + - - +
1042B LYS 3.8 16.4 + - - -
1043B GLY* 4.5 1.8 - - - -
1044B PHE 3.3 30.5 + - - +
1144B GLY 3.8 20.2 + - - -
1145B GLU* 3.9 25.7 - - + +
1147B ALA 5.7 0.6 + - - -
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Residues in contact with TYR1009 (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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1005B LEU 3.1 10.5 + - - +
1006B TRP* 2.9 28.6 + + - +
1008B ARG* 1.3 77.7 - - - +
1010B THR* 1.3 64.6 + - + +
1011B HIS 3.2 0.2 + - - -
1012B ARG* 3.3 4.2 + - - +
1013B ARG* 2.8 39.0 + - - +
1026B GLU* 2.6 34.0 + - - -
1100B ARG* 3.5 30.0 - - + +
1101B VAL 3.7 0.2 - - - -
1102B THR* 2.8 28.9 + - - -
1145B GLU* 3.3 21.3 - - - +
1146B GLN* 3.3 22.7 - - - -
1147B ALA 3.7 13.7 - - - +
1148B TYR* 3.9 11.7 - - + -
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Residues in contact with THR1010 (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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1006B TRP* 2.9 55.6 + - + +
1007B GLU* 3.5 12.3 + - - +
1009B TYR* 1.3 73.5 - - + +
1011B HIS* 1.3 61.7 + - - +
1013B ARG* 3.4 36.1 + - - +
1014B LYS* 3.2 23.4 + - - +
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Residues in contact with HIS1011 (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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1007B GLU 3.1 20.0 + - - +
1008B ARG* 3.8 5.6 + - - +
1010B THR* 1.3 75.7 + - - +
1012B ARG* 1.3 69.2 + - - +
1014B LYS* 3.1 12.8 + - + +
1015B GLU* 3.1 49.1 + - + +
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Residues in contact with ARG1012 (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 ARG 3.2 15.6 + - - +
1009B TYR 3.8 2.9 - - - +
1011B HIS* 1.3 80.5 + - - +
1013B ARG* 1.3 63.0 + - - +
1015B GLU* 2.9 41.4 + - - +
1016B VAL* 3.0 35.2 + - - +
1019B GLU* 4.8 10.3 + - - -
1123B HIS* 3.9 15.4 - - - +
1143B ARG* 3.1 42.5 - - + +
1145B GLU* 3.9 22.0 - - + +
1146B GLN* 3.0 45.9 + - + -
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Residues in contact with ARG1013 (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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1006B TRP* 4.5 8.7 - - - -
1009B TYR* 2.8 27.1 + - + +
1010B THR* 3.4 35.2 + - - +
1011B HIS 3.1 0.2 - - - -
1012B ARG* 1.3 77.1 - - - +
1014B LYS* 1.3 57.7 + - - +
1016B VAL* 3.4 2.4 + - - +
1017B SER* 3.0 30.7 + - - -
1024B ALA* 3.5 25.9 - - + +
1026B GLU* 2.9 37.2 + - - -
1100B ARG* 4.4 5.3 - - - +
1102B THR* 3.5 22.0 - - - +
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Residues in contact with LYS1014 (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 THR 3.2 15.5 + - - +
1011B HIS* 3.1 12.6 + - + +
1013B ARG* 1.3 75.8 - - - +
1015B GLU* 1.3 65.1 + - - +
1017B SER* 3.8 5.9 - - - -
1018B GLU* 2.7 53.7 + - + +
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Residues in contact with GLU1015 (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 HIS* 3.1 43.6 + - + +
1012B ARG* 2.9 42.0 + - - +
1014B LYS* 1.3 77.7 - - - +
1016B VAL* 1.3 63.1 + - - +
1018B GLU* 3.4 7.0 + - - +
1019B GLU* 3.3 29.3 + - - +
1143B ARG* 4.5 6.2 + - - -
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Residues in contact with VAL1016 (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 ARG* 3.0 51.6 + - + +
1013B ARG 3.8 3.8 - - - +
1015B GLU* 1.3 75.7 - - - +
1017B SER* 1.3 64.9 + - - +
1019B GLU* 3.1 14.1 + - - +
1020B ASN* 3.3 13.2 + - - +
1023B HIS 4.9 0.2 - - - +
1024B ALA* 4.3 2.9 - - - +
1102B THR* 3.7 21.8 - - + -
1104B GLY* 3.5 32.1 - - - +
1123B HIS* 3.7 20.5 - - + +
1146B GLN* 4.1 6.5 - - - +
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Residues in contact with SER1017 (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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1013B ARG* 3.0 18.9 + - - -
1014B LYS* 3.8 7.9 - - - -
1015B GLU 3.3 0.2 - - - -
1016B VAL* 1.3 79.7 - - - +
1018B GLU* 1.3 57.9 + - - +
1020B ASN 3.2 6.1 + - - -
1022B ASN* 2.7 50.3 + - - +
1023B HIS 3.4 11.7 + - - +
1024B ALA* 3.9 15.5 + - - -
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Residues in contact with GLU1018 (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 LYS* 2.7 57.0 + - + +
1015B GLU* 3.9 5.8 - - - +
1017B SER* 1.3 78.1 - - - +
1019B GLU* 1.3 60.4 + - + +
1020B ASN 3.3 1.4 + - - -
1021B HIS* 4.5 3.8 + - - -
1022B ASN* 4.6 13.9 + - - +
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Residues in contact with GLU1019 (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 ARG* 4.8 9.6 + - - -
1015B GLU* 3.3 19.6 + - - +
1016B VAL* 3.1 9.4 + - - +
1018B GLU* 1.3 77.7 - - + +
1020B ASN* 1.3 57.8 + - - +
1021B HIS 4.0 0.7 - - - -
1105B LYS* 6.0 0.2 - - - +
1123B HIS* 2.8 40.3 + - + +
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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