Contacts of the strand formed by residues 142 - 145 (chain A) in PDB entry 2H07
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 VAL 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ILE* 3.5 27.8 - - + +
126A THR* 4.4 11.0 - - + -
129A LEU* 4.6 2.7 - - + -
135A GLN* 3.1 38.8 + - + +
138A PHE* 3.6 35.9 - - + -
140A ILE 3.5 9.4 + - - +
141A PRO* 1.3 78.8 - - - +
143A ASP* 1.3 73.7 + - - +
100B LYS* 3.0 28.0 + - - +
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Residues in contact with ASP 143 (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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123A HIS* 2.8 29.4 + - + +
124A ILE 2.9 13.4 + - - +
125A ILE* 3.5 11.4 - - + +
126A THR* 3.1 26.9 + - - +
141A PRO* 6.0 0.6 - - - +
142A VAL* 1.3 79.3 - - - +
144A ASN* 1.3 60.2 + - - +
145A LEU* 3.7 3.4 + - + +
303A THR* 4.2 7.1 + - - -
309A VAL* 4.5 29.3 - - + +
313A PHE* 5.5 7.6 - - + -
1004A SO4 5.2 3.3 + - - -
100B LYS* 4.7 4.9 + - - -
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Residues in contact with ASN 144 (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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126A THR* 3.7 4.2 - - - +
127A MET 3.7 1.7 - - - -
128A ASP* 3.1 12.9 + - - +
129A LEU* 2.9 54.4 + - + +
132A ALA* 5.0 2.6 - - - +
135A GLN* 3.3 22.6 - - + +
142A VAL 4.0 1.4 + - - -
143A ASP* 1.3 70.9 - - - +
145A LEU* 1.3 61.8 + - - +
146A TYR* 3.4 32.6 + - - +
313A PHE* 3.4 12.3 - - - -
1006A SO4 3.5 25.7 + - - -
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Residues in contact with LEU 145 (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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125A ILE* 4.0 16.2 - - + -
126A THR 2.9 14.5 + - - +
127A MET* 3.8 13.7 - - + -
128A ASP* 2.8 30.0 + - - +
143A ASP* 4.6 5.6 - - + +
144A ASN* 1.3 76.8 - - - +
146A TYR* 1.3 61.9 + - - +
295A ILE* 3.8 16.8 - - + +
296A LEU* 3.6 31.9 - - + -
299A ALA* 4.0 13.5 - - + -
309A VAL* 4.2 12.6 - - + -
312A LEU* 4.1 30.5 - - + -
313A PHE* 4.4 8.7 - - + -
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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