Contacts of the strand formed by residues 146 - 154 (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 GLN 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D LEU* 4.1 11.6 - - - +
110D GLU 5.5 2.1 - - - +
137D PRO* 4.0 13.1 - - - +
138D TRP* 5.4 1.0 + - - +
141D SER* 3.1 42.3 + - - -
142D GLU* 4.7 0.2 - - - +
144D MET* 3.2 27.5 + - + +
145D GLU* 1.3 82.4 - - - +
147D GLU* 1.3 62.2 + - - +
148D CYS* 4.8 0.2 - - - -
167D LEU 4.5 0.3 - - - +
168D PRO* 4.5 1.9 - - - +
169D SER* 3.5 41.9 + - - +
191D CYS* 3.8 23.3 - - + +
192D ILE 3.4 17.0 - - - +
194D SER* 4.2 5.5 - - - -
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Residues in contact with GLU 147 (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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146D GLN* 1.3 74.3 - - - +
148D CYS* 1.3 66.7 + - - +
166D HIS* 3.3 50.2 + - + +
167D LEU 3.5 6.1 - - - +
191D CYS* 3.4 1.4 - - - -
192D ILE* 3.0 47.4 + - + +
194D SER* 4.0 20.2 + - - +
195D SER 5.8 0.2 + - - -
200D TRP* 4.0 7.9 - - + -
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Residues in contact with CYS 148 (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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146D GLN* 4.8 0.7 - - - -
147D GLU* 1.3 78.6 - - - +
149D GLU* 1.3 63.4 + - - +
165D PHE 3.9 0.3 - - - -
166D HIS 3.4 7.5 + - - -
167D LEU* 2.7 47.8 + - + +
168D PRO 3.9 18.2 - - - +
169D SER* 4.1 12.3 - - - -
189D MET* 4.1 14.6 - - + -
190D ARG 3.2 5.4 - - - +
191D CYS* 2.0 47.3 - - - -
200D TRP* 4.6 1.1 - - - -
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Residues in contact with GLU 149 (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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148D CYS* 1.3 76.1 - - - +
150D LEU* 1.3 59.1 + - - +
163D LEU* 4.0 8.4 - - + +
164D VAL 3.4 7.6 - - - +
165D PHE* 3.8 34.6 - - + -
166D HIS 5.1 1.1 - - - +
167D LEU* 4.7 0.4 - - - -
189D MET* 3.2 7.2 - - - +
190D ARG* 2.6 57.5 + - - -
200D TRP* 3.2 35.1 - - + -
203D TRP* 3.5 18.5 - - + -
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Residues in contact with LEU 150 (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* 4.0 13.7 - - + -
133D LEU* 4.0 16.8 - - + -
149D GLU* 1.3 73.5 - - - +
151D ARG* 1.3 68.5 + - - +
152D TYR* 4.7 2.9 - - + -
162D THR 4.0 0.2 - - - +
163D LEU* 3.7 2.8 - - - +
164D VAL* 3.1 42.8 + - + +
167D LEU* 3.5 21.7 - - + +
174D PHE* 3.9 28.3 - - + -
176D LEU* 4.6 10.3 - - + -
187D LEU* 4.5 6.1 - - + -
188D GLN 3.4 15.3 - - - +
189D MET* 3.3 23.3 - - + +
203D TRP* 4.7 0.7 - - - -
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Residues in contact with ARG 151 (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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150D LEU* 1.3 77.0 - - - +
152D TYR* 1.3 60.3 + - - +
161D TRP* 3.4 53.2 - - + +
162D THR 3.4 7.6 - - - +
163D LEU* 4.1 11.2 - - + -
187D LEU* 3.4 5.0 - - - +
188D GLN* 2.8 61.3 + - + +
203D TRP* 3.5 63.4 - - + +
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Residues in contact with TYR 152 (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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70A LEU* 4.8 10.7 - - - +
150D LEU* 4.7 4.9 - - + -
151D ARG* 1.3 76.9 - - - +
153D GLN* 1.3 62.9 + - - +
154D PRO* 5.8 0.7 - - + -
161D TRP* 3.5 3.8 - - - -
162D THR* 2.9 68.4 + - + +
164D VAL* 3.8 21.9 - - + +
176D LEU* 3.6 37.2 - - + +
177D CYS 4.6 5.5 + - - -
178D GLY 5.7 1.1 - - - -
179D LEU* 3.6 28.3 - - + -
185D TYR* 4.5 7.2 - + + -
186D THR 3.4 9.9 - - - +
187D LEU* 4.0 17.0 - - + -
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Residues in contact with GLN 153 (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* 1.3 76.3 - - - +
154D PRO* 1.3 80.8 + - + +
155D GLN* 4.8 3.8 - - - +
156D LEU 5.7 1.3 - - - +
159D ALA* 3.2 21.8 + - - +
160D ASN 3.1 44.4 - - - +
161D TRP* 3.5 35.3 - - + +
185D TYR* 3.1 8.5 - - - -
186D THR* 3.0 37.7 + - - +
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Residues in contact with PRO 154 (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* 4.9 1.1 - - + +
153D GLN* 1.3 96.5 + - + +
155D GLN* 1.3 61.1 + - - +
156D LEU* 3.0 23.9 + - + +
158D GLY 5.3 5.8 - - - +
160D ASN* 4.4 8.1 - - + +
162D THR* 5.7 2.2 - - - +
181D GLN* 3.7 24.7 - - + +
182D ALA* 3.4 20.9 - - + -
184D VAL 3.9 1.1 - - - +
185D TYR* 3.1 34.2 - - + +
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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