Contacts of the strand formed by residues 1036 - 1043 (chain A) in PDB entry 1HXK
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 THR1036 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TRP* 4.1 14.8 - - + -
214A TYR* 2.6 35.0 + - - -
218A LYS* 3.5 24.4 - - - +
978A VAL* 3.6 25.1 - - + -
979A LEU 3.2 13.5 - - - +
980A HIS* 2.8 18.5 - - - -
1014A LEU* 3.8 17.8 - - + +
1035A GLU* 1.3 77.0 - - - +
1037A ALA* 1.3 62.2 + - - +
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Residues in contact with ALA1037 (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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978A VAL* 3.5 4.2 - - - +
979A LEU* 2.8 34.7 + - - +
1011A ARG* 4.1 13.0 - - + +
1012A THR 5.5 0.2 - - - -
1014A LEU* 3.8 6.3 - - - -
1031A VAL* 3.3 26.6 - - + +
1035A GLU* 5.1 4.0 - - + +
1036A THR* 1.3 74.5 - - - +
1038A ALA* 1.3 59.8 + - - +
1039A TYR* 4.0 19.5 - - + +
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Residues in contact with ALA1038 (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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977A TYR 3.1 10.8 - - - +
978A VAL* 4.6 2.7 - - + -
1011A ARG* 3.4 9.1 - - - +
1012A THR* 2.9 33.9 + - - +
1013A THR 3.4 25.4 - - - +
1014A LEU* 3.8 17.5 - - + +
1016A PHE* 3.8 9.9 - - + -
1037A ALA* 1.3 74.9 - - - +
1039A TYR* 1.3 65.3 - - - +
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Residues in contact with TYR1039 (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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975A VAL 3.8 0.7 - - - +
976A GLY* 3.3 2.1 - - - -
977A TYR* 2.7 35.8 + - - +
979A LEU* 4.6 19.1 - - + -
999A VAL* 4.1 22.2 - - + -
1000A CYS* 4.4 5.6 - - - -
1010A GLU 3.2 6.1 - - - +
1011A ARG* 2.9 41.0 + - + -
1012A THR 4.5 0.4 - - - +
1016A PHE* 4.0 0.3 - - - -
1023A LEU* 3.6 33.0 - - + -
1028A ALA* 3.7 18.2 - - + -
1029A PRO* 2.6 34.4 + - + +
1030A GLU 4.6 0.7 + - - -
1031A VAL* 4.1 4.1 - - + +
1037A ALA* 4.0 18.9 - - + +
1038A ALA* 1.3 79.4 - - - +
1040A VAL* 1.3 65.5 + - - +
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Residues in contact with VAL1040 (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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965A LEU* 3.8 14.1 - - + -
974A ARG* 3.7 46.9 - - + +
975A VAL 3.2 9.0 - - - +
976A GLY* 4.1 0.7 - - - -
1000A CYS* 4.3 2.5 - - - -
1008A ARG 4.0 0.5 - - - +
1009A CYS* 3.6 1.9 - - - -
1010A GLU* 2.9 40.5 + - - +
1012A THR* 3.7 24.9 - - + -
1016A PHE* 3.8 20.0 - - + -
1039A TYR* 1.3 79.4 - - - +
1041A SER* 1.3 64.5 + - - +
1042A SER* 4.1 2.8 + - - +
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Residues in contact with SER1041 (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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974A ARG* 3.3 4.7 - - - -
975A VAL* 2.9 37.7 + - - +
977A TYR* 3.8 14.0 + - - -
999A VAL 4.7 0.3 + - - -
1000A CYS* 3.7 35.7 + - - -
1006A VAL* 4.4 0.4 - - - -
1008A ARG 3.4 7.2 - - - -
1039A TYR 4.2 0.2 - - - -
1040A VAL* 1.3 74.8 - - - +
1042A SER* 1.3 61.2 + - - +
1043A HIS* 2.7 29.4 + - - -
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Residues in contact with SER1042 (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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972A THR* 3.8 11.4 - - - +
973A GLN 3.2 5.2 - - - -
974A ARG* 4.0 15.6 + - - +
1006A VAL* 3.4 6.1 - - - +
1007A ALA* 2.7 31.1 + - - -
1008A ARG* 2.9 51.8 + - - +
1010A GLU* 4.3 6.9 + - - -
1040A VAL* 4.8 1.4 + - - +
1041A SER* 1.3 71.7 - - - +
1043A HIS* 1.3 59.2 + - - +
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Residues in contact with HIS1043 (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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964A ARG* 5.8 0.4 - - - -
971A LYS 3.9 0.5 - - - +
972A THR* 3.5 7.5 - - - +
973A GLN* 2.8 48.4 + - + +
975A VAL* 4.5 11.4 - - + -
1000A CYS 4.0 2.9 - - - -
1003A LEU* 3.4 41.3 - - + +
1004A PRO 2.9 22.1 + - - +
1005A ASN* 3.2 7.6 - - + +
1006A VAL* 3.5 16.7 - - + -
1007A ALA* 4.8 0.7 - - - -
1041A SER* 2.7 42.0 + - - -
1042A SER* 1.3 76.6 - - - +
1044A SER* 1.3 65.2 + - - +
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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