Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 3CS0
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 TYR 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LEU* 5.8 0.3 - - - +
161A GLY 4.9 6.1 - - - -
162A ASP* 1.3 78.3 - - - +
164A THR* 1.3 66.0 + - - +
180A GLY 3.5 14.4 - - - -
181A ILE* 3.6 18.6 - - + -
216A ASN* 4.1 16.5 - - - +
217A LEU* 3.8 41.5 + - + -
222A ILE* 5.1 0.7 - - - +
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Residues in contact with THR 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 TYR* 1.3 83.3 - - - +
165A VAL* 1.3 65.2 + - - +
179A SER* 3.4 4.2 - - - -
180A GLY 2.8 35.2 + - - +
181A ILE 4.3 0.4 - - - -
182A VAL* 3.6 32.1 - - + +
201A THR* 3.1 21.4 + - - +
203A ALA* 4.3 2.6 - - - +
214A LEU* 3.9 19.5 - - + -
215A VAL 3.4 6.1 - - - -
216A ASN* 4.9 0.2 - - - +
222A ILE* 3.9 17.5 - - + -
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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
----------------------------------------------------------
15A LEU* 4.0 25.6 - - + -
18A MSE 3.8 20.6 - - + -
19A LEU* 4.1 15.3 - - + -
164A THR* 1.3 79.1 - - - +
166A ALA* 1.3 60.4 + - - +
167A ILE* 4.1 16.4 - - + -
177A VAL* 4.9 4.3 - - + -
178A THR 3.4 10.3 - - - +
179A SER* 4.1 4.9 - - - +
213A ALA 4.1 0.3 - - - +
214A LEU* 3.5 4.3 - - - +
215A VAL* 2.9 52.6 + - + +
217A LEU* 4.3 8.5 - - + -
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Residues in contact with ALA 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 THR 4.3 0.4 + - - -
165A VAL* 1.3 70.2 - - - +
167A ILE* 1.3 63.0 + - - +
176A THR 3.7 1.2 - - - +
177A VAL* 3.3 4.0 - - - +
178A THR* 2.7 49.0 + - - +
203A ALA* 4.3 8.7 - - + +
204A ALA 4.5 5.8 - - - +
205A ILE* 4.5 5.6 - - + -
209A ASN* 5.6 3.4 - - - +
213A ALA 3.3 5.4 - - - -
214A LEU* 3.7 12.3 - - + -
225A ASN* 3.6 20.0 - - - +
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Residues in contact with ILE 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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19A LEU* 4.1 15.3 - - + -
22A VAL* 4.0 26.9 - - + -
23A MSE 4.8 8.1 - - + -
26A VAL* 3.8 22.0 - - + +
165A VAL* 4.1 14.8 - - + -
166A ALA* 1.3 79.0 - - - +
168A GLY* 1.3 62.2 + - - +
175A GLU* 3.8 31.0 - - + +
176A THR 3.4 10.8 - - - +
177A VAL* 4.3 10.5 - - + -
209A ASN* 4.4 3.1 - - - +
212A GLY* 3.4 3.8 - - - -
213A ALA* 2.9 32.8 + - + +
215A VAL* 4.4 12.1 - - + -
225A ASN* 4.7 1.4 - - - +
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Residues in contact with GLY 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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26A VAL* 4.5 5.2 - - - -
89A SER* 3.6 15.3 - - - -
167A ILE* 1.3 79.9 - - - +
169A ASN* 1.3 59.3 + - - -
170A PRO* 3.2 10.3 - - - +
174A GLY 3.3 0.5 - - - +
175A GLU* 3.7 4.4 - - - -
176A THR 2.8 32.3 + - - +
209A ASN* 3.6 10.1 + - - -
212A GLY* 4.6 1.1 - - - -
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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