Contacts of the strand formed by residues 176 - 187 (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 THR 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ALA 3.7 1.2 - - - +
167A ILE* 3.4 5.1 - - - +
168A GLY 2.8 31.7 + - - -
170A PRO* 3.4 34.1 - - + +
173A LEU* 4.7 9.4 - - - +
174A GLY 3.0 9.9 + - - -
175A GLU* 1.3 76.8 + - - +
177A VAL* 1.3 64.6 + - - +
178A THR* 3.8 22.4 + - + -
209A ASN* 5.0 1.7 - - - +
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Residues in contact with VAL 177 (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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15A LEU* 5.5 4.9 - - + -
19A LEU* 3.9 28.5 - - + -
23A MSE 4.0 28.3 - - + -
165A VAL* 4.9 7.4 - - + -
166A ALA 3.3 7.2 - - - +
167A ILE* 4.3 12.3 - - + -
175A GLU 4.9 4.0 - - - +
176A THR* 1.3 78.9 - - - +
178A THR* 1.3 74.6 + - - +
179A SER* 6.1 0.2 - - - -
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.4 3.1 - - - +
166A ALA* 2.7 41.2 + - - +
176A THR* 3.8 19.7 - - + -
177A VAL* 1.3 83.4 - - - +
179A SER* 1.3 58.7 + - - +
203A ALA* 4.0 0.8 - - - +
204A ALA* 2.7 48.2 + - + +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.2 23.6 - - - +
164A THR 3.4 12.3 - - - -
165A VAL* 4.2 5.8 - - - -
177A VAL* 6.1 0.2 - - - -
178A THR* 1.3 76.2 - - - +
180A GLY* 1.3 59.2 + - - +
202A ASP 4.4 1.7 - - - +
203A ALA* 3.4 16.5 - - - -
204A ALA 4.5 1.2 + - - -
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Residues in contact with GLY 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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163A TYR* 3.5 9.0 - - - -
164A THR* 2.8 30.2 + - - +
179A SER* 1.3 76.6 - - - +
181A ILE* 1.3 70.6 + - - +
202A ASP* 3.3 13.5 - - - -
203A ALA* 3.5 6.7 - - - +
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Residues in contact with ILE 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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160A VAL* 5.0 3.1 - - + +
161A GLY* 4.4 11.4 - - - +
162A ASP 3.3 10.8 - - - +
163A TYR* 3.6 28.3 - - + -
164A THR* 3.6 3.3 + - - -
180A GLY* 1.3 80.0 - - - +
182A VAL* 1.3 72.7 + - - +
183A SER* 3.2 8.8 + - - +
201A THR* 2.8 24.4 + - - -
202A ASP* 2.7 26.7 + - - +
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Residues in contact with VAL 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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158A LEU* 4.2 15.5 - - + -
159A ARG 3.7 10.1 - - - +
160A VAL* 2.4 54.0 - - + +
162A ASP* 2.8 19.3 + - + +
164A THR* 3.6 22.0 - - + +
181A ILE* 1.3 75.6 - - - +
183A SER* 1.3 61.1 + - - +
184A ALA 3.8 8.5 - - - +
185A LEU* 3.8 24.0 - - + -
199A ILE* 4.3 13.0 - - + -
200A GLN 3.5 5.6 - - - +
201A THR* 4.7 0.9 - - - -
222A ILE* 4.9 0.2 - - + -
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Residues in contact with SER 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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160A VAL* 3.7 12.4 - - - +
181A ILE* 3.2 8.0 + - - +
182A VAL* 1.3 74.2 - - - +
184A ALA* 1.3 60.4 + - - +
187A ARG* 5.2 0.3 + - - -
200A GLN* 2.5 37.4 + - - -
201A THR* 3.9 1.1 - - - -
202A ASP* 3.6 31.0 + - - +
237A GLY 4.9 1.6 + - - -
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Residues in contact with ALA 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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160A VAL* 3.5 9.4 - - - +
182A VAL* 3.4 1.9 - - - +
183A SER* 1.3 83.1 - - - +
185A LEU* 1.3 73.9 + - - +
187A ARG* 3.5 43.1 - - + +
198A PHE 4.8 0.2 - - - -
200A GLN* 2.9 37.3 + - + +
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Residues in contact with LEU 185 (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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155A SER 5.9 0.7 - - - +
158A LEU* 3.3 40.8 - - + +
159A ARG* 4.2 8.1 - - - -
160A VAL* 4.2 10.1 - - + +
182A VAL* 3.8 17.5 - - + -
184A ALA* 1.3 84.5 - - - +
186A GLY* 1.3 66.0 + - - +
187A ARG* 3.4 12.5 + - - -
198A PHE 4.1 1.3 - - - -
199A ILE* 4.2 23.1 - - + -
319A SER* 5.1 3.8 + - - -
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Residues in contact with GLY 186 (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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185A LEU* 1.3 74.0 - - - +
187A ARG* 1.3 67.5 + - - +
188A SER* 3.3 8.5 + - - -
197A ASN* 3.1 29.2 + - - +
198A PHE 3.2 9.1 + - - -
199A ILE* 6.0 0.2 - - - +
319A SER* 4.5 17.7 + - - -
320A SER* 5.1 3.5 + - - -
322A ALA* 5.8 0.3 - - - +
323A ALA* 5.7 1.6 + - - +
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Residues in contact with ARG 187 (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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183A SER 5.2 0.2 + - - -
184A ALA* 3.5 26.2 - - + +
185A LEU 3.4 6.3 + - - -
186A GLY* 1.3 76.6 - - - +
188A SER* 1.3 60.7 + - - +
190A LEU* 6.3 0.9 - - + -
197A ASN* 3.7 0.5 + - - -
198A PHE* 2.8 40.6 + - + +
200A GLN* 2.8 38.1 + - + +
240A PHE* 3.9 22.2 - - + -
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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