Contacts of the strand formed by residues 185 - 193 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D LEU* 4.7 5.2 - - + -
152D TYR* 4.5 5.4 - + + -
153D GLN* 3.1 24.5 - - - -
154D PRO* 3.1 28.3 - - + -
178D GLY 4.4 1.6 + - - -
179D LEU* 3.5 42.7 - - + +
180D HIS 3.2 8.7 + - - -
181D GLN* 3.2 30.9 + - - +
182D ALA 3.5 20.0 - - - -
184D VAL* 1.3 81.7 - - - +
186D THR* 1.3 61.8 + - - +
187D LEU* 3.5 15.3 - - + +
207D LEU 3.4 0.7 - - - +
208D GLN* 3.3 3.9 - - - -
209D LEU 2.9 35.0 + - - +
211D PRO* 3.5 20.0 - - + -
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D TYR* 3.4 5.5 - - - +
153D GLN* 3.0 37.5 + - - +
155D GLN* 4.0 26.2 + - - +
161D TRP* 3.7 23.8 - - + -
185D TYR* 1.3 70.1 - - - +
187D LEU* 1.3 68.9 + - - +
188D GLN* 4.7 2.9 - - + +
206D GLY* 4.1 19.5 - - - -
207D LEU 3.1 9.6 - - - +
208D GLN* 4.4 7.4 - - + +
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Residues in contact with LEU 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU* 4.3 9.7 - - + +
131D LEU* 4.3 13.9 - - + -
133D LEU* 3.6 39.9 - - + -
150D LEU* 4.5 5.4 - - + -
151D ARG 3.4 5.8 - - - +
152D TYR* 4.0 10.1 - - + -
161D TRP* 5.1 0.2 - - - -
176D LEU* 4.3 17.5 - - + -
185D TYR* 3.5 26.2 - - + +
186D THR* 1.3 83.0 - - - +
188D GLN* 1.3 67.6 + - - +
205D PRO 4.0 1.2 - - - +
206D GLY* 3.6 0.2 - - - -
207D LEU* 2.7 44.3 + - + +
209D LEU* 4.4 10.1 - - + -
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Residues in contact with GLN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU* 4.2 4.0 - - - -
150D LEU* 3.4 6.8 - - - +
151D ARG* 2.8 60.9 + - + +
161D TRP* 3.7 12.5 - - + -
186D THR* 4.7 5.3 - - + +
187D LEU* 1.3 79.9 - - - +
189D MET* 1.3 61.8 + - - +
203D TRP* 3.8 28.5 + - + +
204D SER* 2.7 32.9 + - - +
205D PRO* 4.2 1.2 - - - +
206D GLY* 3.7 17.9 - - - +
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Residues in contact with MET 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.8 25.7 - - + +
114D LEU* 3.4 14.4 - - + -
135D TRP* 3.4 63.3 - - + -
148D CYS* 4.1 10.5 - - + -
149D GLU 3.2 17.5 - - - +
150D LEU* 3.3 32.8 - - + -
167D LEU* 4.3 1.6 - - + -
188D GLN* 1.3 75.0 - - - +
190D ARG* 1.3 62.5 + - - +
203D TRP* 3.6 2.9 - - - -
204D SER* 2.9 34.3 + - - +
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Residues in contact with ARG 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PRO* 4.1 2.9 - - - -
148D CYS* 3.2 5.0 - - - +
149D GLU* 2.6 65.4 + - + -
189D MET* 1.3 74.6 - - - +
191D CYS* 1.3 62.2 + - - +
200D TRP* 3.1 55.6 - - + +
201D SER* 3.4 19.5 + - - +
202D PRO 3.7 9.2 - - - +
203D TRP* 3.2 51.1 - - + +
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Residues in contact with CYS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 3.8 4.4 - - + +
110D GLU 5.9 0.9 - - - +
112D PRO* 3.4 32.2 - - + +
137D PRO* 6.1 0.7 - - - -
146D GLN* 3.8 22.2 - - + +
147D GLU 3.4 4.9 - - - +
148D CYS* 2.0 46.4 - - - -
169D SER* 5.3 2.7 - - - -
190D ARG* 1.3 74.1 - - - +
192D ILE* 1.3 61.1 + - - +
200D TRP* 3.4 6.3 - - - -
201D SER* 2.9 37.3 + - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 4.0 5.6 - - - -
146D GLN* 3.4 7.5 - - - -
147D GLU* 3.0 46.6 + - + +
191D CYS* 1.3 75.5 - - - +
193D ARG* 1.3 74.2 + - - +
198D GLY* 3.5 21.5 - - - +
199D PHE 3.7 17.7 - - - +
200D TRP* 3.5 48.9 - - + +
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LYS* 4.8 5.9 - - - +
20C GLU* 2.8 38.0 + - - +
78D TYR* 4.0 15.0 - - - -
102D ASP* 5.7 0.6 + - - -
104D MET* 3.4 20.3 + - - +
105D ASP* 3.0 20.6 + - - -
107D VAL* 6.2 1.1 - - - -
109D LEU* 4.1 7.3 - - + +
144D MET* 3.8 32.7 - - + +
145D GLU 3.9 5.6 - - - +
146D GLN* 4.5 1.1 - - - -
192D ILE* 1.3 87.6 - - - +
194D SER* 1.3 69.6 + - - +
195D SER 3.6 2.4 + - - -
196D LEU* 3.5 45.0 - - + +
197D PRO 2.9 28.1 + - - +
198D GLY* 4.7 7.8 - - - -
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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