Contacts of the strand formed by residues 185 - 193 (chain B) in PDB entry 1CD9
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 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B LEU* 4.7 6.5 - - + -
152B TYR* 4.3 13.0 - + - -
153B GLN* 3.2 24.7 - - - -
154B PRO* 3.4 24.5 - - + -
178B GLY 4.9 0.2 + - - -
179B LEU* 3.3 46.7 - - + +
180B HIS 3.3 0.7 + - - -
181B GLN* 3.0 32.5 + - - +
182B ALA 3.5 22.7 - - - -
184B VAL* 1.3 80.9 - - - +
186B THR* 1.3 62.5 + - - +
187B LEU* 3.8 13.2 - - + +
207B LEU 3.6 0.3 - - - +
208B GLN* 3.3 4.5 - - - -
209B LEU 3.0 34.1 + - - +
211B PRO* 3.5 17.3 - - + -
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 3.2 5.4 - - - +
153B GLN* 2.9 35.8 + - - +
155B GLN* 3.8 22.9 + - - +
161B TRP* 3.6 23.1 - - + -
185B TYR* 1.3 73.3 - - - +
187B LEU* 1.3 68.1 + - - +
188B GLN* 4.7 2.5 - - + +
206B GLY* 4.1 19.5 - - - -
207B LEU 3.0 10.5 - - - +
208B GLN* 4.1 8.6 - - + +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 4.2 6.9 - - + +
131B LEU* 4.2 19.7 - - + -
133B LEU* 3.6 39.5 - - + -
150B LEU* 4.1 9.0 - - + -
151B ARG 3.3 7.4 - - - +
152B TYR* 3.8 10.1 - - + -
161B TRP* 5.5 0.2 - - - -
176B LEU* 4.3 18.6 - - + -
185B TYR* 3.8 18.4 - - + +
186B THR* 1.3 81.0 - - - +
188B GLN* 1.3 66.9 + - - +
205B PRO 4.2 0.9 - - - +
206B GLY* 3.5 0.2 - - - -
207B LEU* 2.7 42.7 + - + +
209B LEU* 4.3 12.3 - - + -
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Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 4.1 2.7 - - - -
150B LEU* 3.1 8.4 - - - +
151B ARG* 2.5 65.3 + - + +
161B TRP* 3.7 10.1 - - + -
186B THR* 4.7 4.7 - - + -
187B LEU* 1.3 80.7 - - - +
189B MET* 1.3 62.9 + - - +
203B TRP* 3.7 25.5 + - + +
204B SER* 2.7 34.0 + - - +
205B PRO* 4.5 1.0 - - - +
206B GLY* 3.6 18.3 - - - +
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Residues in contact with MET 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO* 3.8 19.9 - - + +
114B LEU* 3.4 32.1 - - + -
135B TRP* 3.5 57.0 - - + -
148B CYS* 4.1 14.1 - - + -
149B GLU 3.3 14.8 - - - +
150B LEU* 3.7 25.1 - - + -
167B LEU* 4.7 0.7 - - + -
188B GLN* 1.3 75.9 - - - +
190B ARG* 1.3 62.1 + - - +
203B TRP* 3.6 3.8 - - - -
204B SER* 2.9 33.1 + - - +
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Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PRO* 4.1 2.7 - - - -
148B CYS* 3.3 0.5 - - - +
149B GLU* 2.6 61.6 + - + -
189B MET* 1.3 73.7 - - - +
191B CYS* 1.3 67.7 + - - +
200B TRP* 3.2 56.3 - - + +
201B SER* 3.4 21.2 + - - +
202B PRO 3.7 8.5 - - - +
203B TRP* 3.2 49.2 - - + +
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Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 3.9 5.5 - - + +
112B PRO* 3.4 32.1 - - + +
137B PRO* 5.9 1.1 - - - -
146B GLN* 3.6 22.4 - - + +
147B GLU 3.4 4.9 - - - +
148B CYS* 2.1 45.8 - - - -
169B SER* 5.2 1.8 - - - -
190B ARG* 1.3 74.6 - - - +
192B ILE* 1.3 62.0 + - - +
200B TRP* 3.3 6.2 - - - -
201B SER* 2.8 37.8 + - - +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 5.2 - - - -
146B GLN* 3.2 10.1 - - - -
147B GLU* 3.0 43.2 + - + +
191B CYS* 1.3 76.3 - - - +
193B ARG* 1.3 81.3 + - - +
194B SER* 5.5 0.2 - - - -
196B LEU 6.0 0.4 - - - +
198B GLY 3.4 22.2 - - - +
199B PHE* 3.3 23.1 - - - +
200B TRP* 3.5 44.4 - - + +
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 4.8 3.0 - - - +
20A GLU* 2.8 37.6 + - - +
78B TYR* 3.8 15.6 - - - -
104B MET* 3.0 29.4 + - - +
105B ASP* 3.1 16.8 + - - -
107B VAL* 6.3 1.1 - - - -
109B LEU* 4.3 5.9 - - + +
144B MET* 3.6 30.0 - - + +
145B GLU 3.9 4.7 - - - +
146B GLN* 4.2 4.9 - - - -
192B ILE* 1.3 87.9 - - - +
194B SER* 1.3 69.4 + - - +
195B SER 3.6 2.3 + - - -
196B LEU* 3.4 43.3 - - + +
197B PRO 3.0 23.9 + - - +
198B GLY* 4.5 7.6 - - - -
199B PHE 4.8 0.2 + - - -
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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