Contacts of the helix formed by residues 200 - 208 (chain A) in PDB entry 2FV7
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 GLU 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ASN* 1.3 76.3 - - - +
201A SER* 1.3 58.5 + - - +
203A ALA* 3.2 3.8 + - - +
204A GLU* 3.0 32.6 + - - +
211A VAL* 3.4 30.0 - - + +
212A GLY* 3.1 26.2 - - - +
234A ILE* 4.3 0.4 - - - -
235A THR 3.3 7.7 + - - +
236A LEU* 3.4 43.7 - - + +
239A GLU* 5.8 0.5 - - - +
401A ADP 5.8 0.4 - - - +
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Residues in contact with SER 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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199A ASN* 3.2 16.7 + - - -
200A GLU* 1.3 77.3 - - - +
202A GLU* 1.3 64.9 + - - +
204A GLU* 3.5 15.8 + - - +
205A ILE* 3.2 33.0 + - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 4.5 4.2 + - - -
177A ASN* 4.1 2.8 + - - -
178A PRO 4.0 4.5 - - - +
179A ALA* 3.0 33.0 - - - +
180A PRO* 4.5 3.5 - - + +
181A ALA* 3.7 28.0 - - + +
198A CYS* 3.5 21.3 - - + +
199A ASN* 2.8 44.2 + - - +
201A SER* 1.3 76.7 + - - +
203A ALA* 1.3 63.7 + - - +
205A ILE* 3.2 4.9 + - + +
206A LEU* 3.0 30.8 + - + +
404A MG 4.2 5.8 - - - -
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Residues in contact with ALA 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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198A CYS* 3.8 10.0 - - - -
199A ASN 2.9 18.2 + - - +
200A GLU 3.2 5.1 + - - +
202A GLU* 1.3 77.3 - - - +
204A GLU* 1.4 51.5 + - - +
206A LEU* 3.5 4.4 + - - +
207A THR* 2.8 40.7 + - - +
211A VAL* 4.1 11.7 - - + -
220A ALA* 4.4 2.9 - - + -
224A LEU* 4.9 2.9 - - + -
234A ILE* 3.5 31.6 - - + -
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Residues in contact with GLU 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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200A GLU 3.0 18.5 + - - +
201A SER* 3.7 17.0 - - - +
202A GLU 3.3 0.2 - - - -
203A ALA* 1.4 71.7 - - - +
205A ILE* 1.3 59.7 + - + +
207A THR* 4.2 0.2 - - - -
208A GLY* 2.8 31.5 + - - -
209A LEU 3.1 23.7 + - - +
210A THR* 3.6 12.1 - - - +
211A VAL* 2.9 36.8 + - + +
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Residues in contact with ILE 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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181A ALA* 3.6 35.4 - - + +
182A ILE 4.0 1.1 - - - -
183A ALA* 3.8 38.4 - - + +
201A SER* 3.2 20.3 + - - +
202A GLU* 3.2 8.6 + - + +
204A GLU* 1.3 77.8 - - + +
206A LEU* 1.3 61.1 + - - +
207A THR 3.6 0.7 + - - -
208A GLY* 4.2 3.1 + - - -
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Residues in contact with LEU 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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178A PRO* 3.8 28.9 - - + -
181A ALA* 4.2 5.6 - - + -
182A ILE 3.2 34.3 - - - +
183A ALA 4.9 5.8 - - - +
185A LEU* 4.1 20.0 - - + -
190A TYR* 4.2 5.4 - - - +
196A PHE* 3.9 17.7 - - + -
198A CYS* 4.5 4.9 - - - -
202A GLU 3.0 23.3 + - - +
203A ALA* 4.1 3.6 - - - +
205A ILE* 1.3 79.1 - - - +
207A THR* 1.3 56.3 + - - +
224A LEU* 4.2 13.2 - - + -
227A ARG* 2.7 33.2 + - - +
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Residues in contact with THR 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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203A ALA 2.8 23.4 + - - +
204A GLU* 4.2 0.3 - - - -
206A LEU* 1.3 82.9 - - + +
208A GLY* 1.3 62.9 + - - +
209A LEU* 3.2 38.6 + - - +
220A ALA* 3.9 22.6 - - + +
223A VAL* 4.2 14.2 - - + +
224A LEU* 3.9 23.8 - - + -
227A ARG* 4.3 8.2 + - - +
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Residues in contact with GLY 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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204A GLU 2.8 15.9 + - - -
205A ILE 4.2 2.9 + - - -
206A LEU 3.8 0.6 - - - -
207A THR* 1.3 77.9 - - - +
209A LEU* 1.3 64.1 + - - +
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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