Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 1SY6
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS* 4.1 12.8 - - + -
136A GLN 3.8 21.8 - - - +
137A TYR* 4.4 9.6 - - - -
138A PRO* 5.0 1.1 - - + -
140A SER* 3.1 18.3 + - - +
141A GLU* 1.3 75.3 - - - +
143A LEU* 1.3 73.5 + - - +
144A TRP* 3.7 27.4 - - + +
162A SER* 4.4 8.3 + - - -
164A GLU 3.9 21.7 + - - +
165A ASP* 4.6 8.5 - - + -
183A CYS* 3.9 14.1 - - + -
184A TYR 3.9 8.1 - - - +
185A PRO* 4.8 10.1 - - + -
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Residues in contact with LEU 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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141A GLU* 3.8 13.5 - - + +
142A ILE* 1.3 82.0 - - - +
144A TRP* 1.3 64.2 + - - +
183A CYS* 3.1 7.1 - - - +
184A TYR* 2.9 71.4 + - + +
186A ARG* 3.8 58.8 - - + +
187A GLY 5.4 0.2 - - - +
101H ASP* 4.6 5.4 - - - +
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Residues in contact with TRP 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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121A TYR* 3.8 22.4 - + - -
132A LEU* 3.9 30.5 - - + -
133A THR 4.1 1.1 - - - -
134A CYS* 3.7 37.5 - - + -
142A ILE* 3.7 13.4 - - + +
143A LEU* 1.3 81.0 - - - +
145A GLN* 1.3 65.4 + - - +
150A ASN* 3.4 8.7 - - - +
151A ILE* 3.2 38.8 + - + +
162A SER* 4.3 18.4 + - - -
164A GLU 4.9 1.8 + - - -
165A ASP 4.0 7.6 - - - -
166A HIS 4.7 1.6 - - - -
167A LEU* 3.7 47.1 - - + +
181A TYR* 4.8 3.6 - + + -
182A VAL 3.3 24.0 - - - -
183A CYS* 3.8 12.3 - - + -
184A TYR* 4.2 3.8 + - - -
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Residues in contact with GLN 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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0A MET* 3.6 12.4 - - + +
144A TRP* 1.3 76.0 - - - +
146A HIS* 1.3 59.5 + - - +
147A ASN 4.1 0.2 - - - -
148A ASP* 3.4 27.0 - - - +
149A LYS* 3.3 5.2 - - - +
150A ASN* 3.2 34.3 + - - +
151A ILE* 4.3 4.3 - - - -
180A TYR 3.7 0.2 - - - +
181A TYR* 3.4 8.8 - - - -
182A VAL* 3.1 40.9 + - + +
184A TYR* 3.5 10.6 + - + -
190A PRO* 3.5 28.9 - - - +
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Residues in contact with HIS 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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145A GLN* 1.3 72.3 - - - +
147A ASN* 1.3 99.7 + - + +
148A ASP 3.2 0.4 - - - -
149A LYS* 2.8 24.4 + - - +
151A ILE* 3.6 28.2 - - + +
176A GLU 3.4 25.1 - - - -
177A GLN* 3.6 14.5 + - + +
178A SER 3.1 13.9 + - - -
180A TYR 3.3 12.8 - - - -
181A TYR* 3.6 21.7 + + + -
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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