Contacts of the strand formed by residues 1020 - 1029 (chain A) in PDB entry 1TXD
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 MET1020 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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983A ASN* 2.8 45.5 + - - +
986A ARG* 5.0 6.5 - - - -
987A LEU* 3.4 38.7 - - + +
990A TYR* 3.7 11.4 - - + -
1019A LYS* 1.3 75.6 - - - +
1021A ILE* 1.3 64.6 + - - +
1022A HIS* 3.7 16.2 - - - +
1023A GLU* 3.8 27.8 - - - +
1041A LEU* 3.6 41.3 - - + -
1042A LEU 4.0 1.1 - - - +
1043A LEU* 3.8 10.3 - - + -
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Residues in contact with ILE1021 (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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983A ASN* 5.5 1.1 + - - -
1019A LYS* 3.2 24.2 - - + +
1020A MET* 1.3 77.0 - - - +
1022A HIS* 1.3 67.1 + - + +
1042A LEU* 2.9 31.0 + - + +
1043A LEU 3.8 0.7 - - - -
1044A GLU* 3.6 30.7 - - + +
1126A LEU* 4.4 17.1 - - + +
1130A MET* 3.8 30.1 - - + -
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Residues in contact with HIS1022 (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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1020A MET* 3.7 9.3 - - - +
1021A ILE* 1.3 79.9 - - - +
1023A GLU* 1.3 90.7 + - - +
1041A LEU* 3.7 0.7 - - - -
1042A LEU* 3.0 44.3 + - + +
1119A GLU* 4.1 9.8 - - + +
1122A VAL* 3.3 20.6 - - + +
1123A TRP* 3.6 35.8 - + + -
1126A LEU* 3.2 32.3 - - + -
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Residues in contact with GLU1023 (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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986A ARG* 3.6 26.9 + - - -
990A TYR* 2.2 35.6 + - - -
1020A MET* 3.8 14.0 - - - +
1022A HIS* 1.3 99.7 + - - +
1024A GLY* 1.3 59.5 + - - +
1039A TYR* 2.5 19.3 + - - +
1040A THR 3.4 13.2 - - - +
1041A LEU* 3.9 9.4 - - + -
1119A GLU* 4.5 1.0 - - - +
1123A TRP* 3.7 1.1 - - - -
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Residues in contact with GLY1024 (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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1023A GLU* 1.3 77.2 - - - +
1025A PRO* 1.3 73.8 - - - +
1026A LEU 3.4 1.0 + - - -
1039A TYR* 3.5 15.0 - - - -
1040A THR* 2.9 33.1 + - - +
1119A GLU* 4.1 5.2 - - - -
1123A TRP* 3.4 11.1 - - - -
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Residues in contact with PRO1025 (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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1024A GLY* 1.3 81.7 - - - +
1026A LEU* 1.3 66.3 + - - +
1038A LEU 3.5 12.6 - - - +
1039A TYR* 4.1 13.4 - - + -
1114A ALA* 4.4 3.8 - - - +
1115A GLN* 3.5 44.2 - - - +
1119A GLU* 4.3 15.8 - - - +
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Residues in contact with LEU1026 (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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1024A GLY 3.4 2.6 + - - -
1025A PRO* 1.3 78.9 - - - +
1027A VAL* 1.3 71.6 + - - +
1037A ASP* 4.3 0.5 - - - +
1038A LEU* 2.9 34.3 + - + +
1040A THR* 3.4 40.2 - - + +
1047A LEU* 5.5 1.1 - - + -
1097A LEU* 6.4 1.3 - - + -
1112A LEU* 4.1 29.8 - - + +
1113A VAL 3.8 4.9 - - - +
1114A ALA* 4.0 17.9 - - + +
1123A TRP* 3.5 44.9 - - + +
1127A ILE* 6.2 0.9 - - + -
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Residues in contact with VAL1027 (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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1026A LEU* 1.3 78.2 - - - +
1028A TRP* 1.3 71.8 + - - +
1029A LYS* 4.1 3.1 - - + +
1035A THR* 4.4 20.9 - - + -
1036A ILE 3.8 6.3 - - - +
1037A ASP* 4.2 16.8 - - + +
1038A LEU* 4.5 1.1 - - - +
1112A LEU* 3.2 12.9 - - - +
1113A VAL* 2.9 50.5 + - + +
1115A GLN* 6.0 5.4 - - + +
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Residues in contact with TRP1028 (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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1027A VAL* 1.3 80.8 - - - +
1029A LYS* 1.3 70.4 + - - +
1030A VAL* 3.0 29.8 + - + +
1035A THR* 3.6 1.8 - - - -
1036A ILE* 3.1 62.7 + - + +
1038A LEU* 3.9 24.9 - - + -
1049A LEU* 4.8 10.3 - - + -
1060A ARG 5.3 5.6 - - - -
1061A CYS 5.3 12.8 - - - -
1076A PHE* 4.3 29.2 - + + -
1077A SER 5.3 1.1 - - - -
1078A PRO* 5.9 1.8 - - + -
1109A ILE 5.0 1.4 + - - -
1110A TYR* 3.7 42.8 - + - +
1111A GLU 3.4 15.9 - - - +
1112A LEU* 4.0 9.9 - - + -
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Residues in contact with LYS1029 (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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1027A VAL* 4.1 4.2 - - + +
1028A TRP* 1.3 77.6 + - - +
1030A VAL* 1.3 63.1 + - - +
1031A ASN* 3.1 18.4 - - - +
1032A ARG* 3.5 40.4 - - - +
1034A LYS 4.1 6.1 - - - +
1035A THR* 4.8 7.9 - - + -
1111A GLU* 3.2 58.8 + - + +
1113A VAL* 4.9 10.0 - - + +
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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