Contacts of the strand formed by residues 1038 - 1043 (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 LEU1038 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A PRO* 3.5 8.7 - - - +
1026A LEU* 2.9 33.0 + - + +
1027A VAL 4.6 2.7 - - - +
1028A TRP* 3.9 27.1 - - + -
1036A ILE* 3.2 28.5 + - + +
1037A ASP* 1.3 73.3 - - - +
1039A TYR* 1.3 58.8 + - - +
1040A THR* 3.7 21.1 - - - +
1049A LEU* 3.8 28.5 - - + -
1050A LEU 3.1 30.5 - - - +
1051A GLN* 4.4 2.0 - - + -
1052A LYS* 5.5 2.0 - - - -
1112A LEU* 4.2 9.2 - - + -
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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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990A TYR* 3.6 11.9 + + - -
1023A GLU* 2.5 46.3 + - + +
1024A GLY* 3.5 23.0 + - - -
1025A PRO* 4.1 11.7 - - + -
1038A LEU* 1.3 72.6 - - - +
1040A THR* 1.3 63.1 + - - +
1041A LEU* 3.5 23.3 - - + -
1050A LEU* 3.0 39.4 + - + +
1051A GLN* 4.8 1.2 - - - +
1052A LYS* 3.7 43.7 - - + +
1057A LEU* 5.1 12.8 - - + -
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Residues in contact with THR1040 (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* 3.4 4.7 - - - -
1024A GLY 2.9 27.7 + - - -
1026A LEU* 3.4 36.4 - - + +
1038A LEU* 3.7 10.7 - - - +
1039A TYR* 1.3 77.4 + - - +
1041A LEU* 1.3 70.3 + - - +
1047A LEU* 4.0 11.2 - - + -
1048A VAL 3.4 11.2 - - - +
1049A LEU* 3.7 20.9 - - + +
1123A TRP* 3.5 23.0 - - + -
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Residues in contact with LEU1041 (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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990A TYR* 4.0 15.5 - - + -
1015A LEU* 4.1 24.2 - - + -
1020A MET* 3.6 34.1 - - + -
1022A HIS 3.7 3.1 - - - -
1023A GLU* 3.9 3.1 - - + -
1039A TYR* 3.5 29.8 - - + -
1040A THR* 1.3 86.7 - - - +
1042A LEU* 1.3 60.6 + - - +
1043A LEU* 3.6 8.5 + - + -
1046A ILE 3.8 0.5 - - - +
1047A LEU* 3.5 1.6 - - - -
1048A VAL* 2.9 41.2 + - + +
1050A LEU* 3.5 28.5 - - + -
1057A LEU* 6.1 0.2 - - + -
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Residues in contact with LEU1042 (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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1021A ILE* 2.9 35.5 + - + -
1022A HIS* 3.0 26.9 + - + +
1041A LEU* 1.3 69.4 - - - +
1043A LEU* 1.3 82.8 + - - +
1046A ILE 4.2 0.7 - - - +
1047A LEU* 3.9 14.8 - - + -
1082A LEU* 3.8 21.8 - - + -
1123A TRP* 3.8 20.6 - - + -
1126A LEU* 3.6 33.9 - - + +
1127A ILE* 3.7 20.9 - - + +
1130A MET* 4.2 6.1 - - + -
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Residues in contact with LEU1043 (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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987A LEU* 4.3 5.6 - - + -
1015A LEU* 3.9 30.1 - - + +
1018A ARG* 3.7 33.2 - - + -
1019A LYS 3.6 6.1 - - - +
1020A MET* 3.8 37.7 - - + +
1021A ILE* 3.8 5.4 - - - +
1041A LEU* 4.0 11.9 - - + +
1042A LEU* 1.3 98.0 - - - +
1044A GLU* 1.3 69.0 + - - +
1045A ASP 3.1 2.2 + - - -
1046A ILE* 2.9 33.4 + - + +
1048A VAL* 4.0 3.1 - - + -
1082A LEU* 3.5 1.0 - - - +
1130A MET* 4.3 1.0 - - - +
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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