Contacts of the helix formed by residues 354 - 359 (chain A) in PDB entry 1VLP
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 354 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.5 23.4 - - - +
178A GLY* 3.5 9.2 - - - -
330A LEU 5.1 2.8 + - - +
352A GLY 3.9 2.6 + - - -
353A ILE* 1.3 72.3 - - - +
355A THR* 1.3 60.6 + - - +
356A ASN 3.2 1.7 - - - +
357A PHE* 2.8 25.8 + - - +
358A THR 3.4 7.6 + - - -
500A PO4 3.2 19.0 + - - -
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Residues in contact with THR 355 (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 GLY* 4.2 1.6 - - - -
181A ARG* 3.6 34.4 + - + +
354A GLY* 1.3 70.9 - - - +
356A ASN* 1.3 63.8 + - - +
358A THR* 3.9 7.4 - - - -
359A ASN* 2.9 45.4 + - + +
373A PRO* 4.3 17.3 - - + -
500A PO4 3.1 30.2 + - - -
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Residues in contact with ASN 356 (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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163A LYS* 2.7 53.6 + - - +
330A LEU 3.3 22.3 + - - +
331A ASN* 3.8 27.4 - - - +
332A VAL* 4.8 2.4 + - - +
353A ILE* 4.3 9.3 - - + +
354A GLY 3.1 1.8 + - - +
355A THR* 1.3 78.1 - - - +
357A PHE* 1.3 53.7 + - - +
359A ASN 5.4 0.2 - - - -
360A ASP* 3.2 23.4 + - - +
500A PO4 4.6 1.8 + - - -
109B GLU* 4.3 12.2 + - - +
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Residues in contact with PHE 357 (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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156A GLN* 4.6 3.6 - - - +
159A GLN* 5.7 0.9 + - - -
160A ALA* 3.9 26.0 - - + -
163A LYS* 4.0 23.1 + - + +
164A ALA 4.7 1.6 - - - -
167A LEU* 4.2 12.3 - - + -
174A PHE* 3.7 29.8 - + - -
176A GLU* 4.3 11.2 - - + -
191A ILE* 3.3 36.7 - - + +
195A ILE* 3.8 30.1 - - + -
332A VAL* 6.0 0.2 - - + -
353A ILE* 3.4 43.3 - - + +
354A GLY 2.8 11.5 + - - +
356A ASN* 1.3 81.4 - - - +
358A THR* 1.3 63.3 + - + +
359A ASN 3.5 0.6 + - - -
360A ASP* 4.6 3.1 + - - +
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Residues in contact with THR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN* 5.7 0.2 - - - -
176A GLU* 3.1 27.6 - - - +
178A GLY* 2.8 34.8 + - - +
181A ARG 4.0 2.4 - - - -
182A ARG* 3.5 14.0 + - - -
183A ARG* 3.1 23.6 + - - +
187A ALA* 3.9 9.3 - - - +
188A GLN* 3.9 21.3 - - + +
191A ILE* 3.9 13.9 - - + -
354A GLY 3.4 2.8 + - - -
355A THR* 3.3 3.5 + - - -
357A PHE* 1.3 78.4 - - + +
359A ASN* 1.3 57.9 + - - +
360A ASP 3.9 0.7 - - - -
361A PHE* 3.9 4.1 - - - -
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Residues in contact with ASN 359 (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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140A SER* 3.8 8.7 + - - -
144A PHE* 3.9 8.3 - - - -
181A ARG* 2.9 28.8 + - - +
183A ARG* 2.9 52.0 + - - +
355A THR* 2.9 27.4 + - + +
356A ASN* 5.4 0.2 - - - -
358A THR* 1.3 75.2 - - - +
360A ASP* 1.3 56.2 + - - +
361A PHE* 3.8 4.8 + - - -
370A LYS* 4.5 5.0 + - - -
371A SER 5.1 0.2 - - - +
373A PRO* 3.6 35.2 - - - +
374A LEU 4.8 1.0 + - - +
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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