Contacts of the strand formed by residues 145 - 148 (chain A) in PDB entry 7EHI
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 TRP 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.8 38.4 - + - -
140A VAL* 4.9 2.5 - - + +
143A THR* 3.3 19.7 - - + +
144A VAL* 1.3 80.1 - - - +
146A TYR* 1.3 60.7 + - - +
199A ILE* 4.2 1.6 - - - +
201A GLY* 3.3 33.7 - - - -
202A ILE 3.6 24.0 - - - -
203A TYR* 4.1 2.5 - - + -
247A ARG* 4.4 5.6 - - + -
248A VAL 5.0 0.4 - - - -
249A MET* 3.7 28.3 - - + -
341A ALA* 4.5 4.7 - - + -
370A TYR* 4.0 16.1 - + - -
433A PHE* 3.4 26.5 - + + -
468A VAL* 3.7 27.7 - - + +
469A PRO 2.9 11.0 + - - -
470A SER* 3.3 20.6 - - - +
471A ILE* 2.8 25.6 + - - +
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A TRP* 1.3 74.4 - - - +
147A GLN* 1.3 62.8 + - - +
148A ILE* 3.7 18.1 + - + -
153A PHE* 3.5 22.6 - + - -
193A HIS* 4.2 1.0 + - - -
194A LEU* 3.5 26.2 - - + -
197A LEU* 3.7 23.1 - - + -
199A ILE* 3.8 23.8 - - + -
201A GLY 2.8 8.1 + - - +
202A ILE* 3.3 7.4 - - + +
203A TYR 2.9 21.3 + - - +
470A SER* 4.4 0.9 - - - -
471A ILE* 3.3 20.9 - - + -
473A TYR* 3.4 32.0 - - + -
474A GLY 3.5 2.6 + - - -
476A GLU* 2.7 36.8 + - - -
491A MET* 3.8 2.1 - - - +
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Residues in contact with GLN 147 (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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146A TYR* 1.3 72.4 - - - +
148A ILE* 1.3 60.8 + - - +
203A TYR* 3.3 38.8 - - + +
205A ASN* 3.0 23.0 + - - +
392A MET* 4.9 3.5 - - - +
433A PHE* 5.4 0.7 - - - -
435A THR* 4.8 4.2 + - - +
437A ASP 4.6 2.3 - - - +
438A SER* 3.8 15.8 - - - -
439A HIS* 3.0 33.3 + - - +
470A SER* 4.1 9.5 + - - +
471A ILE 2.8 15.1 + - - +
472A TYR* 3.6 22.8 - - + +
473A TYR* 2.9 31.7 + - - +
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Residues in contact with ILE 148 (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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146A TYR* 3.7 30.3 - - + -
147A GLN* 1.3 71.9 - - - +
149A PHE* 1.4 59.9 + - - +
150A PRO* 3.3 12.3 - - + +
153A PHE* 3.6 40.8 - - + -
187A ILE* 3.9 40.8 - - + -
194A LEU* 4.2 6.5 - - + -
202A ILE* 3.9 20.9 - - + -
203A TYR 2.8 9.1 + - - -
204A LEU* 3.6 10.8 - - + -
205A ASN* 3.1 28.3 + - - -
473A TYR* 4.5 2.2 - - - -
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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