Contacts of the strand formed by residues 146 - 154 (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 GLN 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 14.4 - - + +
110B GLU 5.7 0.5 - - - +
137B PRO* 4.1 13.0 - - - +
138B TRP* 5.3 1.2 + - - +
141B SER* 3.3 40.5 + - - -
144B MET* 3.3 24.2 + - + +
145B GLU* 1.3 82.0 - - - +
147B GLU* 1.3 60.7 + - - +
167B LEU 4.4 0.2 - - - +
168B PRO* 4.4 1.7 - - - +
169B SER* 3.5 41.5 + - - +
191B CYS* 3.6 24.0 - - + +
192B ILE 3.2 20.9 - - - +
193B ARG* 4.2 0.4 - - - -
194B SER* 4.0 6.2 + - - +
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Residues in contact with GLU 147 (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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146B GLN* 1.3 74.1 - - - +
148B CYS* 1.3 65.0 + - - +
149B GLU* 6.4 0.2 - - + -
166B HIS* 3.4 50.3 + - - +
167B LEU 3.4 6.3 - - - +
191B CYS* 3.4 1.4 - - - -
192B ILE* 3.0 47.5 + - + +
194B SER* 4.3 18.7 + - - +
200B TRP* 3.9 9.7 - - + -
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Residues in contact with CYS 148 (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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135B TRP* 5.0 0.2 - - - -
147B GLU* 1.3 77.3 - - - +
149B GLU* 1.3 63.6 + - - +
166B HIS 3.6 5.4 + - - -
167B LEU* 2.8 49.0 + - + +
168B PRO 3.9 16.8 - - - +
169B SER* 4.0 16.6 - - - -
189B MET* 4.1 16.4 - - + -
190B ARG 3.3 5.2 - - - +
191B CYS* 2.1 46.4 - - - -
200B TRP* 4.6 0.9 - - - -
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Residues in contact with GLU 149 (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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147B GLU* 6.4 0.2 - - + -
148B CYS* 1.3 74.8 - - - +
150B LEU* 1.3 58.5 + - - +
163B LEU* 4.3 8.0 - - + +
164B VAL 3.4 8.7 - - - +
165B PHE* 3.6 35.6 - - + -
166B HIS 5.0 1.6 - - - +
167B LEU* 4.5 0.4 - - - -
189B MET* 3.3 6.1 - - - +
190B ARG* 2.6 58.2 + - - -
200B TRP* 3.3 35.6 + - + -
203B TRP* 3.5 17.4 - - + -
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Residues in contact with LEU 150 (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* 4.6 2.2 - - + -
133B LEU* 4.1 13.5 - - + -
149B GLU* 1.3 74.0 - - - +
151B ARG* 1.3 71.1 + - - +
152B TYR* 4.4 15.9 - - + -
162B THR 4.0 0.3 - - - +
163B LEU* 3.7 4.2 - - - +
164B VAL* 3.1 38.2 + - + +
167B LEU* 3.6 17.8 - - + +
174B PHE* 4.0 26.2 - - + -
176B LEU* 4.6 4.3 - - + -
187B LEU* 4.1 17.9 - - + -
188B GLN 3.1 26.2 - - - +
189B MET* 3.7 20.9 - - + +
203B TRP* 4.2 1.6 - - - -
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Residues in contact with ARG 151 (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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150B LEU* 1.3 74.6 - - - +
152B TYR* 1.3 60.3 + - - +
161B TRP* 3.4 56.9 - - + +
162B THR 3.4 7.6 - - - +
163B LEU* 4.2 11.0 - - + +
186B THR 3.8 0.5 - - - +
187B LEU* 3.3 5.2 - - - +
188B GLN* 2.5 73.2 + - + +
203B TRP* 3.2 63.0 - - + +
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Residues in contact with TYR 152 (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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150B LEU* 4.4 6.5 - - + -
151B ARG* 1.3 77.7 - - - +
153B GLN* 1.3 62.2 + - - +
161B TRP* 3.4 2.7 - - - -
162B THR* 3.0 66.7 + - + +
164B VAL* 3.8 23.8 - - + +
176B LEU* 3.7 38.1 - - + +
177B CYS 5.5 0.7 + - - -
179B LEU* 3.6 29.1 - - + +
185B TYR* 4.3 12.8 - + + -
186B THR 3.2 10.3 - - - +
187B LEU* 3.8 17.7 - - + -
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Residues in contact with GLN 153 (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* 1.3 79.2 - - - +
154B PRO* 1.3 77.6 - - + +
155B GLN* 5.4 0.9 - - - -
159B ALA* 3.2 35.8 + - + +
160B ASN 3.6 9.6 - - - +
161B TRP* 3.4 45.6 + - + +
185B TYR* 3.2 8.0 - - - -
186B THR* 2.9 39.6 + - - +
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Residues in contact with PRO 154 (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* 5.9 0.2 - - + -
153B GLN* 1.3 90.5 - - + +
155B GLN* 1.3 59.0 + - - +
156B LEU* 3.0 24.4 + - + -
159B ALA* 3.0 22.0 - - + +
160B ASN 4.5 7.2 - - - +
162B THR* 5.8 1.6 - - - +
181B GLN* 3.9 24.5 - - + +
182B ALA* 3.9 15.0 - - + -
184B VAL 3.6 2.9 - - - +
185B TYR* 3.4 34.3 - - + -
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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