Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 2C6V
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 ARG 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ASP 4.8 8.7 + - - -
18A HIS* 4.3 22.6 + - - -
19A PRO* 4.3 26.7 - - - +
99A ILE* 4.4 3.1 - - + -
100A GLN* 6.3 0.8 - - - +
132A GLU* 2.9 58.0 + - + +
134A CYS* 5.6 1.0 - - - -
190A LYS 3.3 2.4 - - - +
191A VAL* 3.6 3.5 - - - -
192A MET* 2.7 64.5 + - + +
194A VAL* 5.8 8.5 - - + +
197A ASP 5.3 4.3 + - - -
198A HIS* 1.3 81.7 - - - +
200A ILE* 1.3 59.7 + - - +
201A GLY 3.4 0.5 + - - -
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Residues in contact with ILE 200 (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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132A GLU* 3.1 7.2 + - - +
133A TYR* 2.9 73.4 + - + +
159A PHE* 3.7 35.0 - - + -
161A LEU* 6.1 2.9 - - + -
167A VAL* 4.6 12.1 - - + -
189A ALA* 3.6 27.1 - - + -
190A LYS 4.0 3.1 - - - -
191A VAL* 5.2 5.6 - - + +
198A HIS* 3.9 5.3 + - + +
199A ARG* 1.3 69.5 - - - +
201A GLY* 1.3 57.5 + - - +
202A ILE* 3.6 21.1 - - + -
218A TYR* 6.0 0.2 - - + -
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Residues in contact with GLY 201 (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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99A ILE* 3.9 23.1 - - - -
129A PHE* 4.1 0.7 - - - -
131A SER 3.8 4.5 - - - -
188A TYR 3.3 1.0 - - - +
189A ALA* 3.1 5.0 - - - -
190A LYS* 2.7 44.7 + - - +
192A MET* 5.4 0.4 - - - -
199A ARG 3.4 2.6 + - - -
200A ILE* 1.3 74.6 - - - +
202A ILE* 1.3 60.5 + - - -
203A PHE* 4.0 7.8 + - - -
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Residues in contact with ILE 202 (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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129A PHE* 3.1 8.1 - - - -
130A ILE* 2.7 43.8 + - + -
131A SER 2.8 29.6 + - - +
132A GLU 3.8 2.2 - - - -
133A TYR* 3.7 15.0 - - + +
176A ILE* 4.0 12.8 - - + -
187A CYS* 3.4 41.1 - - + -
188A TYR 3.3 8.1 - - - +
189A ALA* 5.0 0.4 - - - +
200A ILE* 3.6 32.1 - - + +
201A GLY* 1.3 73.4 - - - +
203A PHE* 1.3 55.0 + - - +
216A PHE* 5.9 7.9 - - + -
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Residues in contact with PHE 203 (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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67A TYR* 3.6 39.9 - + - -
71A ARG 5.0 0.9 - - - -
73A CYS* 3.7 21.3 - - + -
81A CYS* 5.1 2.7 - - - -
98A SER* 5.4 0.9 - - - -
99A ILE* 5.1 4.5 - - + -
127A ASN 3.4 20.9 - - - -
128A GLU 3.3 4.3 - - - +
129A PHE* 3.3 43.3 - + + -
130A ILE* 3.5 5.4 - - - -
187A CYS* 3.2 1.6 - - - -
188A TYR* 2.8 34.9 + - + +
190A LYS* 3.4 40.8 - - + -
201A GLY* 4.1 9.4 - - - -
202A ILE* 1.3 74.1 - - - +
204A ALA* 1.3 63.3 + - - +
205A LYS 3.3 0.3 + - - -
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Residues in contact with ALA 204 (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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73A CYS* 4.8 0.3 - - - -
124A VAL* 3.7 14.4 - - + -
125A GLN 3.8 10.1 - - - +
127A ASN* 2.6 32.9 + - - +
128A GLU 2.8 17.3 + - - +
130A ILE* 3.1 7.4 - - + +
186A ASN 3.4 6.7 - - - -
187A CYS* 4.4 0.2 - - - +
203A PHE* 1.3 70.5 - - - +
205A LYS* 1.3 59.5 + - - +
206A ARG 3.5 17.7 - - - +
208A ILE* 3.6 16.8 - - + -
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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