Contacts of the helix formed by residues 354 - 359 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C PHE* 3.5 19.2 - - - +
178C GLY* 3.4 12.6 - - - -
330C LEU 4.9 2.4 + - - +
352C GLY 3.9 3.6 + - - -
353C ILE* 1.3 72.9 - - - +
355C THR* 1.3 60.9 + - - +
356C ASN 3.1 2.4 - - - +
357C PHE* 2.9 22.7 + - - +
358C THR 3.4 7.4 + - - -
500C PO4 3.2 20.6 + - - -
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Residues in contact with THR 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C GLY* 4.1 1.8 - - - -
181C ARG* 3.6 31.6 + - + +
354C GLY* 1.3 72.8 - - - -
356C ASN* 1.3 57.1 + - - +
358C THR* 4.0 7.6 - - - -
359C ASN* 2.8 51.7 + - + +
373C PRO* 4.1 19.1 - - + -
500C PO4 3.1 30.8 + - - -
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Residues in contact with ASN 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C LYS* 2.8 54.3 + - - +
330C LEU 3.3 21.8 - - - +
331C ASN* 3.8 29.3 - - - +
332C VAL* 4.7 2.6 + - - +
353C ILE* 4.2 8.1 - - + +
354C GLY 3.1 1.2 - - - -
355C THR* 1.3 78.6 - - - +
357C PHE* 1.3 54.6 + - - +
359C ASN 5.3 0.4 - - - -
360C ASP* 3.2 28.1 + - - +
370C LYS* 6.0 1.6 - - - +
500C PO4 4.4 3.2 + - - -
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Residues in contact with PHE 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLN* 4.7 2.6 - - - +
159C GLN* 5.6 0.9 + - - -
160C ALA* 4.0 18.3 - - + +
163C LYS* 3.9 39.1 + - + +
164C ALA 4.6 1.8 - - - -
167C LEU* 4.5 5.2 - - + -
174C PHE* 3.7 35.4 - + - -
176C GLU* 4.2 11.7 - - + -
191C ILE* 3.3 39.5 - - + +
195C ILE* 3.9 22.0 - - + -
353C ILE* 3.5 43.2 - - + +
354C GLY 2.9 11.1 + - - +
356C ASN* 1.3 80.0 - - - +
358C THR* 1.3 62.3 + - + +
359C ASN 3.5 0.6 + - - -
360C ASP* 4.6 2.9 + - - +
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Residues in contact with THR 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C GLN* 5.7 0.2 - - - -
176C GLU* 3.1 28.9 - - - +
178C GLY* 2.6 33.8 + - - +
181C ARG 4.0 2.3 - - - -
182C ARG* 3.4 15.4 + - - -
183C ARG* 3.0 23.0 + - - +
187C ALA* 4.1 5.6 - - - +
188C GLN* 3.9 20.6 - - + +
191C ILE* 4.0 14.6 - - + -
354C GLY 3.4 2.8 + - - +
355C THR* 3.3 3.7 + - - -
357C PHE* 1.3 77.5 - - + +
359C ASN* 1.3 58.6 + - - +
360C ASP 3.9 0.9 - - - -
361C PHE* 4.0 6.2 - - - -
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Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C SER* 3.8 3.2 + - - -
144C PHE* 3.6 20.0 - - - -
181C ARG* 2.9 26.5 + - - +
183C ARG* 2.9 45.4 + - - +
355C THR* 2.8 27.4 + - + +
356C ASN* 5.3 0.2 - - - -
358C THR* 1.3 77.2 - - - +
360C ASP* 1.3 57.8 + - - +
361C PHE* 3.9 4.8 + - - -
370C LYS* 4.3 5.5 + - - -
371C SER 5.1 0.3 - - - +
373C PRO* 3.6 35.1 - - - +
374C LEU 4.6 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