Contacts of the strand formed by residues 123 - 127 (chain B) in PDB entry 1D0G
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 ALA 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.4 12.6 - - + -
247A ILE* 4.1 4.9 - - + -
280A VAL* 4.8 6.3 - - + -
281A GLY* 5.5 3.1 - - - +
121B ARG 3.9 1.2 - - - -
122B VAL* 1.3 77.5 - - - +
124B ALA* 1.3 64.0 + - - +
163B PHE* 3.5 19.8 - - + -
165B SER* 2.9 33.9 + - - +
167B LEU* 3.9 4.9 - - - +
277B ALA 3.2 12.6 - - - +
278B PHE* 3.7 11.7 - - + +
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Residues in contact with ALA 124 (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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247A ILE* 3.7 4.9 - - - +
123B ALA* 1.3 79.3 - - - +
125B HIS* 1.3 63.1 + - - +
126B ILE 4.2 0.2 - - - -
163B PHE* 3.4 17.3 - - - +
164B LEU* 3.9 21.8 - - + -
167B LEU* 4.0 20.0 - - + -
174B LEU* 4.1 11.9 - - + -
276B GLY* 3.1 3.5 - - - -
277B ALA 2.9 30.1 + - - +
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Residues in contact with HIS 125 (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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247A ILE* 3.4 20.9 + - + +
248A PHE* 3.5 28.7 - + - -
124B ALA* 1.3 75.3 - - - +
126B ILE* 1.3 61.6 + - - +
127B THR* 4.0 12.2 - - + +
161B HIS 3.2 23.8 - - - -
162B SER* 2.9 20.6 - - - -
163B PHE* 2.9 29.8 + - + +
185B TYR* 2.7 24.2 + + - +
270B HIS 5.1 0.4 + - - -
274B PHE* 3.4 43.9 - + + +
275B PHE 3.6 3.5 + - - -
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Residues in contact with ILE 126 (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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125B HIS* 1.3 79.5 - - - +
127B THR* 1.3 64.7 + - - +
154B TRP* 3.4 29.7 - - + -
155B GLU 4.1 14.6 - - - +
156B SER* 5.0 0.7 - - - -
162B SER* 3.6 3.1 - - - -
163B PHE 4.2 2.7 - - - +
164B LEU* 4.0 28.3 - - + -
169B LEU* 3.4 35.7 - - + -
174B LEU* 4.0 8.5 - - + -
274B PHE* 3.4 5.2 - - - +
275B PHE* 2.8 64.1 + - + +
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Residues in contact with THR 127 (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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125B HIS* 4.0 13.9 - - + +
126B ILE* 1.3 79.6 - - - +
128B GLY* 1.3 61.4 + - - +
154B TRP* 3.5 11.2 - - - -
155B GLU* 2.9 30.4 + - - +
160B GLY* 3.0 29.0 + - - +
161B HIS* 5.6 0.2 - - + -
162B SER* 3.4 12.9 + - - -
270B HIS* 3.4 36.9 - - - +
273B SER 4.0 0.9 - - - -
274B PHE* 3.8 12.1 - - + -
62S ARG* 5.2 1.7 + - - -
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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