Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 2SRT
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 ILE 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TRP* 4.9 14.6 - - + +
97A LEU* 5.0 6.3 - - + -
98A THR 2.8 13.4 + - - +
99A TYR* 3.0 13.3 - - + +
100A ARG 2.8 23.4 + - - -
121A LEU* 5.0 6.1 - - + -
132A PHE* 4.6 16.2 - - + -
140A ALA 4.4 0.2 - - - -
141A ASP* 1.3 83.6 - - + +
143A MET* 1.3 58.8 + - - +
144A ILE* 3.2 27.1 + - + +
176A GLY* 3.3 22.4 - - - +
177A ASP* 5.1 0.4 - - - -
203A ILE* 4.8 6.7 - - + -
206A SER* 4.4 14.1 - - - +
207A LEU* 4.4 22.0 - - + -
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Residues in contact with MET 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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100A ARG* 3.2 31.0 - - + +
102A VAL* 4.4 18.8 - - + -
138A GLY 3.1 27.6 - - - +
139A GLU* 3.8 23.1 - - + +
140A ALA 3.6 19.7 - - - +
141A ASP 3.6 3.6 + - - +
142A ILE* 1.3 70.9 - - - +
144A ILE* 1.3 55.4 + - - +
145A SER* 3.0 7.2 + - - +
177A ASP* 2.6 44.0 - - - +
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Residues in contact with ILE 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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99A TYR* 4.2 7.0 - - + -
100A ARG 2.6 12.9 + - - +
101A ILE* 3.2 11.9 - - + +
102A VAL 2.8 26.3 + - - -
117A VAL* 3.8 38.1 - - + -
121A LEU* 5.9 0.2 - - + -
142A ILE* 3.2 41.5 + - + +
143A MET* 1.3 70.0 - - - +
145A SER* 1.3 61.9 + - - +
146A PHE* 3.6 12.3 - - + -
177A ASP* 4.0 0.4 - - - -
178A ALA* 3.6 16.4 - - + +
180A PHE* 3.5 31.2 - - + -
203A ILE* 4.2 13.7 - - + -
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Residues in contact with SER 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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102A VAL* 2.9 35.2 - - - +
103A ASN* 3.3 7.0 - - - -
143A MET* 3.0 12.7 + - - +
144A ILE* 1.3 71.6 - - - +
146A PHE* 1.3 68.1 + - - +
147A ALA* 5.1 0.2 - - - +
177A ASP* 3.9 7.3 + - - -
178A ALA 3.0 8.3 + - - +
179A HIS* 3.2 30.2 - - - +
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Residues in contact with PHE 146 (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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101A ILE* 4.4 4.3 - - + -
103A ASN* 2.8 46.8 + - - +
104A TYR* 3.7 10.3 - - - -
105A THR* 4.0 9.9 - - + -
113A VAL* 3.6 30.7 - - + -
117A VAL* 6.1 1.3 - - + -
144A ILE* 3.6 16.4 - - + -
145A SER* 1.3 80.5 - - - +
147A ALA* 1.3 65.8 + - - +
180A PHE* 3.1 59.5 - + + +
181A ASP 6.0 0.2 - - - -
182A ASP* 3.3 33.7 - - - +
186A TRP* 6.1 1.1 - + - -
195A LEU* 5.1 4.9 - - + -
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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