Contacts of the strand formed by residues 1016 - 1023 (chain A) in PDB entry 1UX6
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 ARG1016 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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841A ASN* 6.0 1.8 - - - -
843A ASP* 3.5 17.2 + - - +
846A GLU* 2.8 32.7 + - - +
848A GLY* 5.4 0.4 - - - -
1010A GLY 3.9 0.2 - - - +
1012A GLN* 2.8 57.1 + - + +
1013A SER* 3.0 30.1 + - - +
1014A SER 3.6 0.6 - - - -
1015A SER* 1.3 89.2 - - - +
1017A PHE* 1.3 64.0 + - - +
1049A LYS* 4.7 11.1 - - + +
1125A TYR* 3.4 38.8 + - + +
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Residues in contact with PHE1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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947A LEU* 4.3 18.4 - - + -
978A LEU* 4.1 20.2 - - + -
1008A VAL* 3.8 15.3 - - + -
1010A GLY 3.6 9.6 - - - -
1011A TYR* 3.6 29.2 - + + -
1013A SER 3.4 15.9 - - - -
1014A SER* 3.7 21.5 - - - -
1016A ARG* 1.3 75.0 - - - +
1018A TYR* 1.3 72.0 + - - +
1019A VAL* 3.9 15.0 - - + -
1047A VAL 3.8 0.3 - - - -
1048A VAL* 2.8 63.7 + - + +
1058A LEU* 5.1 1.3 - - + -
1062A LEU* 4.6 6.5 - - + -
1125A TYR* 3.4 9.7 - - - -
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Residues in contact with TYR1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A VAL* 3.2 29.1 - - - +
1009A PHE* 3.1 57.4 + + + +
1010A GLY* 4.2 4.7 - - - -
1017A PHE* 1.3 75.5 - - - +
1019A VAL* 1.3 61.2 + - - +
1045A VAL* 5.8 1.3 - - + -
1046A LYS 3.4 6.5 - - - +
1047A VAL* 3.6 26.7 - - + -
1075A LEU* 4.3 5.2 - - + -
1096A HIS* 4.1 7.4 + + - -
1103A ILE* 3.9 21.1 - - + -
1122A ASP* 2.7 38.8 + - - -
1124A THR 3.2 2.8 + - - -
1125A TYR* 3.0 49.4 + + + -
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Residues in contact with VAL1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007A PHE 3.5 10.5 - - - +
1008A VAL* 3.8 5.4 - - + +
1017A PHE* 3.9 11.0 - - + -
1018A TYR* 1.3 76.1 - - - +
1020A VAL* 1.3 67.3 + - - +
1021A MET* 3.8 24.0 + - + -
1044A SER 3.9 0.5 - - - +
1045A VAL* 3.7 1.6 - - - +
1046A LYS* 2.8 52.9 + - + +
1048A VAL* 4.3 15.9 - - + -
1062A LEU* 4.4 2.7 - - + -
1133A PHE* 3.7 37.2 - - + -
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Residues in contact with VAL1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A GLY* 3.0 4.4 - - - -
1007A PHE* 2.8 78.2 + - + +
1009A PHE* 4.2 14.8 - - + -
1019A VAL* 1.3 78.8 - - - +
1021A MET* 1.3 62.8 + - - +
1043A LEU* 3.7 26.2 - - + -
1044A SER 3.3 7.2 - - - +
1045A VAL* 4.3 16.6 - - + -
1094A LEU* 5.0 1.3 - - + -
1103A ILE* 6.2 0.2 - - + -
1105A VAL* 4.2 14.4 - - + -
1107A MET* 4.8 2.0 - - + -
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Residues in contact with MET1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A TYR* 3.5 34.9 - - + -
1005A ALA 3.5 6.3 - - - +
1019A VAL* 3.8 28.9 - - + -
1020A VAL* 1.3 74.8 - - - +
1022A TRP* 1.3 60.1 + - - +
1042A GLY 3.8 1.2 - - - +
1043A LEU* 3.5 5.3 - - - +
1044A SER* 2.8 35.6 + - - +
1046A LYS* 3.5 23.3 - - + -
1062A LEU* 3.2 33.4 - - + +
1133A PHE* 3.8 35.4 - - + -
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Residues in contact with TRP1022 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A PHE* 3.7 22.4 - + + -
1003A ASP 3.1 5.9 - - - +
1004A TYR* 3.4 3.5 - - - -
1005A ALA 2.9 23.8 + - - +
1021A MET* 1.3 75.7 - - - +
1023A LYS* 1.3 66.6 + - - +
1042A GLY 3.3 22.1 - - - -
1043A LEU* 3.8 14.5 - - + +
1082A ILE* 2.7 32.3 + - + -
1083A GLY 4.0 2.7 - - - -
1084A TRP* 3.0 43.4 + + + +
1090A TYR* 3.6 44.6 - + - -
1107A MET* 3.7 30.5 - - + -
1114A MET* 4.1 19.1 - - + -
1115A ALA* 5.2 5.8 - - + -
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Residues in contact with LYS1023 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002A ASP* 3.1 13.0 + - - +
1003A ASP* 2.8 33.7 + - - -
1004A TYR* 3.3 29.1 - - + +
1022A TRP* 1.3 74.2 - - - +
1024A GLN* 1.3 60.7 + - - +
1025A VAL 2.6 27.0 + - - +
1027A GLN* 3.3 15.5 + - - +
1039A GLY 3.4 23.3 - - - +
1040A TYR 3.7 11.7 - - - +
1041A SER* 4.1 0.7 - - - -
1042A GLY 3.0 27.3 + - - -
1063A TRP* 3.4 31.6 - - - +
1083A GLY* 3.3 7.6 - - - -
1084A TRP* 3.6 2.7 - - - -
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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