Contacts of the strand formed by residues 1096 - 1099 (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 GLY1096 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037B ARG 3.4 3.3 + - - +
1038B LEU* 3.2 16.6 - - - +
1039B ALA 3.1 19.6 + - - -
1094B VAL* 3.6 5.1 - - - +
1095B HIS* 1.3 82.0 - - - +
1097B PHE* 1.3 60.8 + - - +
1122B LYS* 3.3 14.4 - - - -
1124B VAL* 3.9 15.7 - - - -
1287B THR* 5.6 2.6 - - - +
1290B SER* 4.8 0.6 - - - -
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Residues in contact with PHE1097 (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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1038B LEU* 4.1 1.3 - - - -
1039B ALA* 3.0 30.1 - - + +
1041B LEU* 5.4 0.2 - - + -
1085B ILE* 3.9 18.4 - - + -
1088B LEU* 3.5 42.4 - - + -
1089B ASN* 3.2 31.6 - - - -
1094B VAL* 4.2 4.0 - - + -
1096B GLY* 1.3 77.0 - - - +
1098B LEU* 1.3 72.0 + - - +
1099B VAL* 4.8 3.4 - - + -
1118B ILE* 3.7 34.5 - - + +
1122B LYS* 3.0 42.5 + - + +
1123B ASP* 4.4 3.3 - - - +
1124B VAL* 3.5 11.6 + - - +
1125B ASP 4.9 0.3 + - - -
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Residues in contact with LEU1098 (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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1038B LEU* 4.6 3.6 - - + -
1039B ALA 3.0 5.5 + - - -
1040B ILE* 3.4 37.1 - - + -
1041B LEU* 2.7 34.0 + - - +
1056B LYS* 4.2 6.1 - - - +
1097B PHE* 1.3 80.0 - - - +
1099B VAL* 1.3 58.7 + - - +
1100B GLN* 3.8 22.9 - - - +
1118B ILE* 4.9 4.0 - - - -
1124B VAL* 4.3 4.7 - - + -
1125B ASP* 3.5 32.5 - - + +
1283B LEU* 3.7 41.3 - - + -
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Residues in contact with VAL1099 (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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1041B LEU* 3.4 25.6 - - + +
1081B VAL* 5.5 0.9 - - + -
1085B ILE* 4.1 22.7 - - + -
1097B PHE* 4.8 3.4 - - + -
1098B LEU* 1.3 81.7 - - - +
1100B GLN* 1.3 62.5 + - - +
1101B LEU* 3.5 18.0 + - + +
1103B LEU* 3.6 29.4 - - + -
1114B VAL* 4.3 13.0 - - + -
1115B ILE* 4.1 13.7 - - + +
1118B ILE* 4.0 21.8 - - + +
1125B ASP* 4.6 4.5 - - - +
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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