Contacts of the strand formed by residues 1191 - 1195 (chain B) in PDB entry 1DIA
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 THR1191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A THR* 3.8 21.5 - - + -
194A THR 3.6 17.9 - - - +
195A CYS* 4.1 9.4 - - - -
196A HIS* 4.2 2.0 + - - -
198A LYS 5.0 0.2 + - - -
199A THR* 2.9 30.9 + - - +
200A ALA 4.6 1.6 + - - -
205A GLU* 3.8 24.0 - - - +
1165B GLY 4.7 3.9 + - - -
1166B ARG 2.8 11.9 + - - -
1167B HIS* 3.3 8.7 - - - +
1168B ALA 2.9 23.2 + - - +
1189B ASN 4.0 0.4 + - - -
1190B ALA* 1.3 70.1 - - - +
1192B VAL* 1.3 60.0 + - - +
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Residues in contact with VAL1192 (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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182A HIS* 5.7 0.2 - - - -
192A VAL 3.4 2.1 - - - +
193A THR* 3.1 3.3 - - - -
194A THR* 2.9 37.0 + - - -
1168B ALA* 3.5 10.1 - - + +
1170B VAL* 4.2 21.1 - - + -
1182B HIS* 3.8 31.3 - - + +
1185B LEU* 3.8 11.9 - - + -
1186B LEU* 3.6 31.0 - - + +
1190B ALA* 3.5 16.5 + - + +
1191B THR* 1.3 75.5 - - - +
1193B THR* 1.3 72.3 + - - +
1194B THR* 4.2 0.9 - - - +
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Residues in contact with THR1193 (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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167A HIS* 4.1 2.2 - - + -
191A THR* 3.8 25.8 - - + -
192A VAL 3.1 5.2 - - - +
193A THR* 2.9 23.3 + - - +
1167B HIS* 2.7 31.1 + - - -
1168B ALA 3.1 7.1 + - - -
1169B VAL* 3.5 11.4 - - + +
1170B VAL 3.1 23.7 + - - +
1192B VAL* 1.3 72.7 - - - +
1194B THR* 1.3 63.3 + - - +
1195B CYS* 3.9 8.4 + - - -
1205B GLU* 3.9 15.0 - - - +
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Residues in contact with THR1194 (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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182A HIS* 4.2 5.8 + - - -
186A LEU* 3.9 27.6 - - + +
191A THR* 3.5 18.2 - - - +
192A VAL 2.9 18.3 + - - -
1170B VAL* 3.6 8.7 - - + +
1172B GLY 3.9 15.9 - - - +
1173B ARG* 4.0 9.9 - - + -
1178B GLY 5.4 2.2 - - - +
1179B ALA* 6.4 0.2 - - - -
1182B HIS* 3.6 34.1 - - + +
1192B VAL* 4.2 1.9 - - - +
1193B THR* 1.3 74.7 + - - +
1195B CYS* 1.3 71.7 + - - +
1196B HIS* 4.2 4.3 - - - -
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Residues in contact with CYS1195 (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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191A THR* 4.0 13.2 - - - -
1169B VAL* 4.0 19.1 - - - -
1170B VAL 2.9 11.0 + - - +
1171B VAL* 4.3 7.2 - - + -
1172B GLY* 2.9 27.8 + - - -
1193B THR* 4.2 4.0 - - - -
1194B THR* 1.3 79.4 - - - +
1196B HIS* 1.3 66.3 + - - +
1199B THR* 3.3 10.1 - - - +
1202B LEU* 3.7 22.2 - - + -
1205B GLU* 3.9 27.8 - - - -
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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