Contacts of the helix formed by residues 198 - 206 (chain A) in PDB entry 5V8V
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 PHE 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A SER* 2.9 19.6 + - - -
197A GLY* 1.3 74.4 - - - -
199A ILE* 1.3 66.7 + - - +
200A GLU* 3.1 15.2 + - - +
201A GLN* 3.1 7.9 + - - +
208A PRO* 3.9 2.2 - - - -
261A LEU* 3.8 19.7 - - + -
264A THR* 4.1 10.1 - - + -
265A GLY* 3.4 38.3 + - - +
266A VAL* 3.4 15.9 - - - +
267A TRP* 3.4 47.1 - + - -
395A ARG* 3.6 36.3 - - - +
398A ASN* 3.9 13.9 - - - -
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Residues in contact with ILE 199 (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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198A PHE* 1.3 72.9 - - - +
200A GLU* 1.3 77.6 + - - +
201A GLN 3.1 0.2 - - - -
202A ALA* 3.1 14.0 + - - +
205A ARG* 3.5 44.2 - - + +
206A VAL 3.5 14.6 - - - +
207A THR* 3.8 23.3 - - + +
208A PRO* 3.6 17.9 - - + +
211A ASP* 4.6 12.1 - - - +
395A ARG* 5.0 2.8 - - - +
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Residues in contact with GLU 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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198A PHE* 3.0 17.9 - - - +
199A ILE* 1.3 89.5 + - - +
201A GLN* 1.3 63.7 + - + +
202A ALA 3.5 0.9 - - - +
205A ARG* 4.1 25.3 + - - +
264A THR* 3.5 24.9 - - - +
265A GLY* 3.7 25.0 - - - +
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Residues in contact with GLN 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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106A GLY 5.5 5.5 + - - +
107A SER* 5.7 2.5 - - - -
108A SER* 3.4 22.9 + - - +
109A ASN* 4.3 1.6 - - - +
198A PHE 3.1 4.3 + - - +
200A GLU* 1.3 81.8 - - + +
202A ALA* 1.3 62.0 + - - +
203A ILE* 3.4 11.8 + - - +
265A GLY 3.3 23.8 - - - +
266A VAL* 4.7 10.8 - - + +
374A PRO* 5.2 8.1 - - - +
375A THR* 3.1 30.0 + - - +
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Residues in contact with ALA 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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108A SER* 3.9 20.4 - - - +
109A ASN* 3.5 10.8 - - - +
198A PHE 3.7 1.0 + - - -
199A ILE* 3.1 17.9 + - - +
200A GLU 3.5 0.7 - - - +
201A GLN* 1.3 76.2 - - - +
203A ILE* 1.3 61.4 + - - +
204A GLY 3.5 0.2 + - - -
205A ARG* 2.9 24.9 + - - -
206A VAL* 3.3 31.0 - - - +
208A PRO* 4.6 0.2 - - + -
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Residues in contact with ILE 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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109A ASN* 3.0 24.2 + - - +
145A LEU* 3.8 14.2 - - + +
146A THR 3.4 23.8 - - - +
147A LEU* 3.5 28.5 - - + -
148A ARG* 5.4 7.4 - - + +
201A GLN 4.4 8.5 - - - +
202A ALA* 1.3 71.1 - - - +
204A GLY* 1.3 64.9 + - - +
205A ARG 3.3 0.7 + - - -
206A VAL* 3.5 9.5 + - - +
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Residues in contact with GLY 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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145A LEU* 5.0 3.6 - - - -
158A LEU* 5.8 3.3 - - - +
202A ALA 3.5 0.2 + - - -
203A ILE* 1.3 76.5 - - - +
205A ARG* 1.3 68.1 + - - +
206A VAL* 3.0 15.1 + - - +
501A NAG 5.2 5.4 + - - -
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Residues in contact with ARG 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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199A ILE* 3.5 36.0 + - + +
200A GLU* 4.1 30.9 + - - +
202A ALA* 2.9 19.0 + - - +
204A GLY* 1.3 77.9 - - - +
206A VAL* 1.3 64.6 + - - +
207A THR* 3.5 2.3 + - - -
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Residues in contact with VAL 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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108A SER 4.9 1.1 - - - +
109A ASN* 4.5 11.4 - - - +
158A LEU* 3.9 33.9 - - + -
172A GLN* 4.6 0.2 - - - +
173A MET* 3.5 44.0 - - + +
199A ILE* 3.5 0.5 - - - +
202A ALA* 3.3 13.1 - - + +
203A ILE 3.5 18.6 + - - +
204A GLY* 4.0 8.5 - - - +
205A ARG* 1.3 80.6 - - - +
207A THR* 1.3 73.4 + - - +
208A PRO* 3.2 10.0 - - - +
501A NAG 6.1 0.7 - - - +
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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