Contacts of the strand formed by residues 59 - 62 (chain B) in PDB entry 1D2H
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 ARG 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B HIS* 1.3 71.9 - - - +
60B VAL* 1.3 59.8 + - - +
80B SER* 3.6 23.6 - - - +
82B THR* 5.6 1.1 - - - -
126B ALA 4.1 8.2 + - - -
127B GLY* 5.4 0.2 - - - -
128B ASP* 4.5 6.9 - - - +
129B GLY 3.7 33.7 + - - +
130B PHE* 3.7 27.7 - - - +
131B ASP* 2.6 56.0 + - - +
132B ALA 3.0 3.3 + - - -
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.2 23.1 - - + -
58B HIS 3.5 16.4 - - - +
59B ARG* 1.3 78.4 - - - +
61B LEU* 1.3 62.3 + - - +
62B ASP* 4.1 0.6 + - - -
74B LEU* 4.4 9.6 - - + -
79B PHE* 4.4 11.4 - - + -
80B SER 3.0 8.6 + - - +
81B VAL* 3.6 6.4 - - + -
82B THR* 3.0 30.1 + - - +
130B PHE* 3.6 4.6 - - - -
132B ALA* 2.7 26.0 - - + +
134B ILE* 3.4 30.3 - - + -
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Residues in contact with LEU 61 (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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60B VAL* 1.3 75.0 - - - +
62B ASP* 1.3 64.9 + - - +
63B VAL* 3.8 16.7 + - + -
82B THR* 3.0 38.1 - - + +
84B VAL* 4.1 17.7 - - + -
120B LEU* 5.2 0.2 - - + -
124B VAL* 3.9 11.2 - - + -
130B PHE* 3.3 28.4 - - + -
132B ALA 3.0 6.3 + - - -
133B VAL* 3.4 11.7 - - + +
134B ILE 3.0 22.4 + - - -
163B MET* 3.6 43.5 - - + -
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Residues in contact with ASP 62 (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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60B VAL 4.1 0.6 + - - -
61B LEU* 1.3 72.3 - - - +
63B VAL* 1.3 59.6 + - - +
64B ALA* 2.8 20.2 + - - +
65B CYS* 3.3 19.8 + - - +
70B ASP* 5.0 3.3 - - - +
71B SER* 3.1 35.8 + - - +
81B VAL* 5.6 0.9 - - + +
82B THR 3.1 7.7 + - - +
83B SER* 3.9 8.3 - - - -
84B VAL* 3.0 29.9 + - - +
134B ILE* 3.2 27.7 - - + +
135B CYS* 4.9 0.7 - - - -
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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