Contacts of the strand formed by residues 188 - 194 (chain A) in PDB entry 1CX4
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 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PHE* 3.9 22.6 - - + -
171A LYS* 5.6 0.6 - - - +
187A ASP* 1.3 112.1 + - - +
189A PHE* 1.3 62.8 + - - +
190A TYR* 3.3 35.2 + - + -
220A GLY 3.6 8.7 - - - +
224A LEU* 3.8 6.2 - - - +
230A ARG* 2.9 18.9 + - - -
245A LEU 3.3 8.5 - - - +
246A ASP* 3.4 17.8 + - - +
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Residues in contact with PHE 189 (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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150A ILE* 4.5 5.2 - - + -
152A LEU* 4.0 13.9 - - + -
153A PHE* 3.8 31.6 - + - -
188A ASN* 1.3 75.4 - - - +
190A TYR* 1.3 60.1 + - - +
191A VAL* 3.8 13.0 - - + -
218A SER* 3.5 27.4 - - - -
219A PHE 3.5 15.7 - - - -
220A GLY 4.2 1.6 - - - -
221A GLU* 3.6 44.0 - - + -
224A LEU* 3.8 5.1 - - + +
243A TRP 3.6 0.7 - - - +
244A GLY* 3.3 5.0 - - - -
245A LEU* 2.9 42.8 + - + +
250A PHE* 3.8 30.3 - + + -
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Residues in contact with TYR 190 (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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169A PHE* 4.9 1.6 - + - -
171A LYS* 3.3 39.8 + - + -
179A VAL* 3.9 14.8 + - + +
180A ILE* 4.1 13.9 - - + -
187A ASP* 4.0 7.7 + - - -
188A ASN* 3.3 46.0 + - + +
189A PHE* 1.3 79.3 - - - +
191A VAL* 1.3 62.5 + - - +
218A SER* 3.0 9.4 - - - -
219A PHE* 2.9 70.8 + + + +
230A ARG* 4.7 2.5 - - - -
242A LEU* 3.8 25.1 - - + -
243A TRP 3.4 1.1 - - - +
244A GLY* 3.9 15.0 - - - -
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Residues in contact with VAL 191 (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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146A ALA* 3.6 34.8 - - + +
147A CYS* 4.3 4.7 - - - -
150A ILE* 4.0 11.2 - - + -
153A PHE* 4.2 10.1 - - + -
168A MET* 3.9 19.7 - - + -
189A PHE* 3.8 22.4 - - + -
190A TYR* 1.3 77.0 - - - +
192A ILE* 1.3 67.8 + - - +
217A GLY 3.6 6.7 - - - +
218A SER* 4.1 4.3 - - - -
242A LEU* 3.5 3.8 - - - -
243A TRP* 2.8 42.3 + - + +
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Residues in contact with ILE 192 (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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146A ALA* 3.8 5.5 - - - +
191A VAL* 1.3 74.7 - - - +
193A ASP* 1.3 56.0 + - - +
194A ARG 3.5 20.6 - - - +
197A PHE* 3.8 17.7 - - + -
213A TYR* 3.4 40.4 - - + -
215A ASN* 3.6 22.9 - - - -
216A ARG* 2.6 44.6 + - - +
217A GLY 2.9 18.3 + - - +
219A PHE* 3.9 12.8 - - + -
241A ALA 4.5 0.2 - - - +
242A LEU* 3.9 18.8 - - + -
243A TRP* 4.7 0.4 - - - -
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Residues in contact with ASP 193 (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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142A ARG* 3.2 40.1 + - - +
146A ALA* 4.2 0.9 - - - +
191A VAL 3.6 1.6 + - - -
192A ILE* 1.3 75.5 - - - +
194A ARG* 1.3 89.0 + - - +
215A ASN* 4.0 3.1 - - - +
216A ARG* 3.6 19.0 + - - +
241A ALA* 3.0 23.0 + - + +
243A TRP* 2.8 33.9 + - + +
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Residues in contact with ARG 194 (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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142A ARG* 3.9 14.8 - - - +
170A GLU* 4.9 0.8 + - - -
172A LEU* 4.3 13.9 - - - +
192A ILE* 3.5 9.5 - - - +
193A ASP* 1.3 103.7 + - - +
195A GLY* 1.3 62.4 + - - +
197A PHE* 4.2 3.3 - - - -
215A ASN* 3.6 13.0 - - - +
239A PRO 5.1 2.4 + - - +
240A GLY* 3.4 11.3 + - - -
241A ALA* 3.1 50.9 + - - +
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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