Contacts of the strand formed by residues 179 - 184 (chain A) in PDB entry 3CL0
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 SER 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.0 1.1 - - - +
177A ALA* 3.5 2.5 - - - +
178A TRP* 1.3 97.6 - - - +
180A ALA* 1.3 63.2 + - - +
194A ILE* 2.9 39.6 + - - +
224A ARG* 3.8 2.9 - - - +
225A THR* 3.1 25.0 + - - -
227A GLU* 2.5 28.2 + - - -
800A G39 4.2 4.0 - - - -
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Residues in contact with ALA 180 (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 PHE* 4.5 5.8 - - + -
134A LEU* 3.9 13.5 - - + -
158A LEU* 3.8 33.4 - - + -
177A ALA* 4.5 1.1 - - + -
179A SER* 1.3 77.3 + - - +
181A SER* 1.3 60.5 - - - +
192A ILE 3.1 13.5 - - - +
225A THR* 3.5 8.2 - - - +
227A GLU* 2.9 40.9 + - - +
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Residues in contact with SER 181 (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 PHE* 3.9 4.7 - - - -
158A LEU* 4.3 2.3 - - - +
180A ALA* 1.3 75.8 - - - +
182A ALA* 1.3 61.4 + - - +
191A THR* 3.6 1.4 - - - -
192A ILE* 2.7 54.0 + - - +
225A THR* 4.0 9.6 - - - +
226A GLN* 3.4 18.3 + - - -
228A SER 2.9 21.4 + - - -
230A CYS* 3.5 8.4 + - - -
239A THR* 3.7 7.4 + - - -
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Residues in contact with ALA 182 (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 PHE* 3.6 21.6 - - + -
123A SER* 3.5 3.9 + - - -
132A PHE* 3.7 30.3 - - + -
158A LEU* 4.9 0.9 - - + -
181A SER* 1.3 80.2 + - - +
183A CYS* 1.3 65.5 + - - +
190A LEU 3.2 13.0 - - - +
191A THR* 3.9 5.6 - - + +
228A SER 3.9 0.2 + - - -
229A GLU* 3.1 24.4 - - - +
230A CYS* 3.4 4.4 - - - -
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Residues in contact with CYS 183 (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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123A SER* 3.6 12.6 - - - +
182A ALA* 1.3 73.5 - - - +
184A HIS* 1.3 57.4 + - - +
189A TRP* 3.6 7.2 - - - -
190A LEU* 2.7 46.2 + - - +
229A GLU* 5.1 0.4 - - - +
230A CYS* 2.0 61.5 - - - +
232A CYS* 3.5 24.5 - - - -
237A CYS* 3.8 9.9 - - - -
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Residues in contact with HIS 184 (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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85A LEU* 3.3 20.3 - - - +
123A SER* 4.5 1.6 + - - -
124A CYS 3.9 3.8 + - - +
125A SER* 3.3 42.1 - - - -
126A HIS* 3.8 8.0 + + - -
183A CYS* 1.3 76.8 - - - +
185A ASP* 1.3 58.4 + - - +
186A GLY* 2.9 49.0 + - - -
187A THR 3.4 12.4 + - - -
188A SER* 3.5 20.8 - - - -
189A TRP* 3.5 36.9 - + + -
232A CYS* 3.7 9.8 - - - +
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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