Contacts of the strand formed by residues 161 - 166 (chain A) in PDB entry 4EO7
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 PHE 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A MET* 5.8 1.3 - - + -
158A PRO* 3.7 28.5 - - + -
159A GLU 4.1 13.9 - - - -
160A ARG* 1.3 78.5 - - - +
162A ASP* 1.3 65.4 + - - +
163A ALA 4.0 5.4 - - - +
190A LYS* 3.5 22.2 - - - +
191A LEU 4.1 0.2 - - - -
192A CYS* 3.8 31.9 - - + -
205A TRP* 3.7 37.2 - + + -
206A SER 4.8 5.4 - - - -
207A ILE* 4.0 22.7 - - + -
215A ARG* 2.8 22.0 + - + +
216A CYS* 3.5 3.3 - - - -
217A ARG* 3.1 30.1 + - - +
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Residues in contact with ASP 162 (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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161A PHE* 1.3 73.5 - - - +
163A ALA* 1.3 64.3 + - + +
188A ARG 4.3 1.4 - - - +
189A LEU* 3.4 15.6 - - + +
190A LYS* 2.7 46.8 + - - +
191A LEU* 4.7 4.9 - - + -
217A ARG* 2.8 42.7 + - - +
218A ARG* 3.1 25.3 + - - +
293A LEU* 3.5 22.6 - - + +
294A SER* 4.6 4.1 - - - +
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Residues in contact with ALA 163 (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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161A PHE* 3.3 1.3 - - - -
162A ASP* 1.3 84.3 - - - +
164A PHE* 1.3 66.5 + - - +
165A ILE* 4.2 0.6 + - + +
190A LYS 3.4 3.1 + - - +
191A LEU* 3.4 16.0 - - + +
192A CYS* 3.0 29.8 + - - +
216A CYS* 4.3 2.9 - - - -
218A ARG 3.1 15.5 - - - +
220A VAL* 4.1 7.4 - - + -
293A LEU* 3.7 26.5 - - + -
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Residues in contact with PHE 164 (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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163A ALA* 1.3 72.4 - - - +
165A ILE* 1.3 76.0 + - - +
166A CYS* 3.7 23.3 + - + -
192A CYS* 3.3 13.5 - - - -
193A VAL* 3.6 4.9 - - - -
194A SER* 3.5 41.1 - - - -
207A ILE* 3.7 19.7 - - + -
212A ILE* 3.5 33.7 - - + -
216A CYS* 3.8 18.3 - - + -
218A ARG 3.0 8.0 + - - +
219A MET* 3.4 18.5 - - + +
220A VAL* 2.8 27.4 + - - +
235A PHE* 4.2 10.1 - + - -
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Residues in contact with ILE 165 (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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163A ALA 4.9 3.6 - - - +
164A PHE* 1.3 87.5 - - - +
166A CYS* 1.3 60.5 + - - +
167A TYR* 3.7 24.9 - - + -
175A VAL* 4.2 8.3 - - + -
178A MET* 3.9 29.2 - - + -
179A ILE* 4.1 30.1 - - + -
182A LEU* 5.6 1.8 - - + -
191A LEU* 4.5 25.6 - - + -
192A CYS 2.9 13.1 + - - +
193A VAL* 4.0 18.0 - - + +
194A SER 5.2 0.2 + - - -
220A VAL* 3.7 18.4 - - + -
222A VAL* 4.4 7.0 - - + -
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Residues in contact with CYS 166 (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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164A PHE* 3.7 20.1 + - + -
165A ILE* 1.3 70.9 - - - +
167A TYR* 1.3 62.6 + - - +
219A MET* 3.9 14.4 - - - -
220A VAL 2.8 16.3 + - - +
221A VAL* 3.7 2.4 - - - -
222A VAL* 3.0 28.1 + - - +
227A TYR* 3.4 23.8 - - - +
232A GLU* 3.5 28.0 - - - -
235A PHE* 4.5 5.4 - - - -
236A GLN* 3.7 9.4 - - + -
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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