Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 5CYO
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 ASN 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A HIS 3.0 22.8 + - - +
135A CYS* 3.4 4.7 - - - -
136A CYS* 2.8 32.1 + - - +
162A VAL* 1.3 77.1 - - - +
164A ILE* 1.3 58.2 + - - +
198A TYR* 4.3 16.4 - - + -
200A GLN* 3.2 21.4 + - - +
273A ILE* 3.1 23.7 + - + +
276A ILE* 3.3 10.8 - - - +
277A THR* 3.0 22.0 + - - +
281A HIS* 3.1 17.7 + - - -
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Residues in contact with ILE 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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136A CYS* 3.5 32.1 - - + +
138A TYR* 4.3 13.7 - - + -
155A MET* 4.5 14.6 - - + +
158A LEU* 3.5 26.7 - - + -
159A SER* 3.8 21.8 - - - +
162A VAL* 3.5 13.6 + - + +
163A ASN* 1.3 77.1 - - - +
165A VAL* 1.3 66.0 + - - +
166A PRO* 4.0 15.3 - - + -
195A ILE* 5.7 0.9 - - + -
196A ASP 4.5 12.0 + - - +
197A VAL* 3.4 11.4 - - + +
198A TYR 2.8 30.7 + - - +
200A GLN* 5.2 0.6 - - - +
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Residues in contact with VAL 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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135A CYS* 3.6 19.7 - - - -
136A CYS 2.9 10.0 + - - -
137A LEU* 3.3 25.6 - - + +
138A TYR 3.1 19.0 + - - -
164A ILE* 1.3 78.8 - - - +
166A PRO* 1.3 67.9 - - + +
167A VAL* 3.8 1.3 + - + +
198A TYR* 3.9 22.0 - - + +
220A ILE* 4.3 7.0 - - + -
222A PHE* 3.7 35.7 - - + -
261A LEU* 4.4 2.9 - - + -
264A LEU* 4.3 13.9 - - + -
265A LEU* 6.2 0.9 - - + -
273A ILE* 5.7 0.9 - - + -
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Residues in contact with PRO 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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138A TYR* 3.4 10.1 - - + +
140A ILE* 3.9 21.8 - - + -
155A MET* 4.2 12.1 - - - -
164A ILE* 3.7 4.2 - - + +
165A VAL* 1.3 93.6 - - - +
167A VAL* 1.3 62.0 + - - +
190A LEU* 4.0 11.7 - - + -
197A VAL* 3.6 31.2 - - + -
220A ILE* 3.5 23.9 - - + +
221A PRO* 3.3 20.8 - - + +
222A PHE 3.4 4.2 + - - -
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Residues in contact with VAL 167 (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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39A LEU* 5.4 0.7 - - + -
137A LEU* 5.3 4.5 - - + -
138A TYR 2.8 8.1 + - - +
139A PHE* 4.0 26.2 - - + -
140A ILE* 2.8 30.0 + - - +
165A VAL 4.7 4.3 - - - +
166A PRO* 1.3 74.7 - - - +
168A ILE* 1.3 67.7 + - - +
169A ALA 3.9 2.0 - - - +
221A PRO* 4.1 2.7 - - - -
222A PHE* 3.4 29.2 - - + +
224A VAL* 3.4 40.8 - - + -
261A LEU* 4.2 14.1 - - + -
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Residues in contact with ILE 168 (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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140A ILE* 3.7 7.0 - - - +
142A ALA* 3.9 8.3 - - + -
167A VAL* 1.3 72.1 - - - +
169A ALA* 1.3 73.4 + - - +
171A ALA* 3.8 7.2 - - + +
174A LEU* 3.9 26.2 - - + -
179A ARG* 4.7 6.7 - - + +
182A PHE* 3.8 20.2 - - + -
183A LYS* 3.8 33.2 - - + -
186A ILE* 4.1 11.7 - - + -
221A PRO* 4.0 21.8 - - + +
222A PHE 2.7 12.7 + - - +
223A ALA* 4.2 5.2 - - + -
224A VAL* 3.2 24.6 + - - +
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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