Contacts of the helix formed by residues 204 - 215 (chain A) in PDB entry 3CP7
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 GLY 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.8 1.9 - - - -
118A ASN* 3.4 20.0 - - - -
202A TYR* 3.2 23.1 + - - -
203A PHE* 1.3 75.2 - - - +
205A SER* 1.3 61.2 + - - -
206A GLY 3.3 3.4 - - - -
207A ALA* 3.4 4.3 + - - +
208A GLN* 2.9 27.4 + - - +
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Residues in contact with SER 205 (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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118A ASN* 3.6 18.9 + - - +
204A GLY* 1.3 70.9 - - - -
206A GLY* 1.3 62.3 + - - +
208A GLN* 3.8 6.2 - - - +
209A GLN* 3.0 45.9 + - - +
218B ASN* 5.2 1.4 + - - -
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Residues in contact with GLY 206 (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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90A HIS* 5.2 3.7 - - - -
92A TYR* 3.4 14.8 - - - -
204A GLY 3.3 0.6 - - - -
205A SER* 1.3 82.4 + - - +
207A ALA* 1.3 56.7 + - - +
210A ASN* 2.9 31.0 + - - +
213B TYR* 3.5 5.9 - - - -
218B ASN* 3.7 30.1 + - - +
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Residues in contact with ALA 207 (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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92A TYR* 3.1 36.8 + - + -
94A PHE* 4.1 3.4 - - + -
117A PHE* 3.6 16.3 - - + -
203A PHE* 4.0 25.1 - - + -
204A GLY 3.4 10.2 + - - +
206A GLY* 1.3 75.1 - - - +
208A GLN* 1.3 58.3 + - - +
210A ASN* 3.4 1.6 + - - +
211A TYR* 2.9 31.0 + - - +
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Residues in contact with GLN 208 (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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117A PHE* 3.5 43.1 - - + +
118A ASN* 3.8 18.9 + - - -
204A GLY 2.9 12.9 + - - +
205A SER* 3.8 7.1 - - - +
206A GLY 3.2 0.2 - - - -
207A ALA* 1.3 76.8 - - - +
209A GLN* 1.3 60.2 + - + +
211A TYR* 3.3 2.1 + - - +
212A ASN* 2.8 49.9 + - - +
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Residues in contact with GLN 209 (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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205A SER* 3.0 32.7 + - - +
208A GLN* 1.3 76.5 - - + +
210A ASN* 1.3 64.9 + - - +
212A ASN* 3.4 12.8 + - - +
213A TYR* 3.1 23.7 + - - +
209B GLN* 5.0 2.0 - - - +
212B ASN* 3.2 31.2 - - + +
213B TYR* 3.9 21.4 - - + +
216B THR* 2.9 31.2 + - - +
218B ASN* 3.5 8.7 + - - -
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Residues in contact with ASN 210 (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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77A VAL* 3.6 26.1 + - - +
78A THR 3.7 7.3 - - - +
79A SER* 3.7 24.0 - - - +
92A TYR* 4.0 13.0 + - + -
94A PHE* 3.8 20.2 - - + -
206A GLY 2.9 17.2 + - - +
207A ALA* 3.7 6.3 - - - +
209A GLN* 1.3 75.0 - - - +
211A TYR* 1.3 58.7 + - - +
213A TYR* 3.3 7.7 + - - +
214A ALA* 2.8 30.8 + - - +
213B TYR* 3.9 26.8 - - + -
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Residues in contact with TYR 211 (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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28A VAL* 4.1 10.5 - - + -
29A ALA* 2.5 31.7 + - - +
30A SER* 4.2 3.5 - - - -
35A THR* 5.1 0.7 - - + -
94A PHE* 3.6 35.8 - + + -
115A ILE* 3.7 26.5 - - + +
117A PHE* 3.6 22.0 - + + -
207A ALA 2.9 18.3 + - - +
208A GLN 3.5 1.6 - - - +
210A ASN* 1.3 73.4 - - - +
212A ASN* 1.3 83.8 + - - +
214A ALA* 4.4 0.9 - - - +
215A SER* 2.8 54.6 + - - -
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Residues in contact with ASN 212 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A GLN* 2.8 44.7 + - - +
209A GLN* 3.7 13.0 - - - +
211A TYR* 1.3 89.5 - - - +
213A TYR* 1.3 59.0 + - - +
215A SER* 3.3 13.5 + - - -
216A THR* 3.0 21.0 + - - +
209B GLN* 3.3 18.8 - - + +
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Residues in contact with TYR 213 (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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77A VAL* 4.0 16.8 - - + -
209A GLN 3.1 15.0 + - - +
210A ASN* 3.5 7.4 - - - +
212A ASN* 1.3 77.7 - - - +
214A ALA* 1.3 60.5 + - - +
216A THR* 3.2 8.9 + - - -
218A ASN* 2.2 85.8 + - + +
78B THR 5.0 2.0 - - - -
79B SER* 3.3 13.0 - - - -
80B ALA* 2.9 20.6 + - + -
81B GLU* 3.7 0.3 + - - -
92B TYR* 5.0 1.2 + - - -
206B GLY 3.4 19.5 - - - -
209B GLN* 3.8 29.4 - - + +
210B ASN* 3.9 25.4 - - + +
213B TYR* 5.6 6.1 - + + -
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Residues in contact with ALA 214 (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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32A ASN* 3.1 17.5 + - - -
35A THR* 4.1 3.1 - - + -
77A VAL* 3.9 26.7 - - + -
94A PHE* 3.5 33.4 - - + -
96A VAL* 3.3 14.0 - - + +
210A ASN 2.8 20.4 + - - +
211A TYR 4.1 1.1 - - - +
213A TYR* 1.3 73.0 - - - +
215A SER* 1.3 57.4 + - - +
216A THR 3.1 2.1 + - - -
217A THR* 3.2 5.7 + - - -
218A ASN 4.3 3.1 - - - +
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Residues in contact with SER 215 (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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30A SER* 3.6 21.1 - - - -
31A ALA 3.5 5.1 + - - -
32A ASN* 3.0 31.3 + - - -
35A THR* 3.5 12.3 - - - -
211A TYR* 2.8 45.1 + - - -
212A ASN* 3.3 11.4 + - - -
213A TYR 3.3 0.2 - - - -
214A ALA* 1.3 76.7 - - - +
216A THR* 1.3 61.4 + - - +
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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