Contacts of the strand formed by residues 397 - 401 (chain B) in PDB entry 2VGZ
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 TYR 397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357B TRP* 3.1 52.9 - + + -
358B ILE 3.1 6.3 - - - -
359B LYS* 3.3 51.3 + - + +
366B VAL* 4.7 3.4 - - - +
383B PRO* 3.7 2.8 - - - +
384B GLY 2.8 23.1 + - - -
388B TYR* 3.6 21.3 - - - -
395B SER* 3.3 13.4 + - - +
396B PRO* 1.3 98.8 - - + +
398B LEU* 1.3 62.5 + - - +
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B LEU 3.5 1.6 - - - +
357B TRP* 3.6 6.8 - - - -
358B ILE* 2.8 60.3 + - + +
360B VAL* 3.9 26.0 - - + -
366B VAL* 4.0 15.0 - - + -
370B ILE* 4.1 14.8 - - + -
381B MET* 3.5 30.3 - - + -
382B LEU 3.1 14.1 - - - +
384B GLY 4.4 0.7 - - - +
397B TYR* 1.3 74.5 - - - +
399B ARG* 1.3 61.8 + - - +
417B LEU* 4.0 21.5 - - + -
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 3.6 11.8 + - - +
37A ALA 3.5 19.8 + - - -
38A GLY 4.0 3.6 + - - -
39A GLY* 4.1 10.9 - - - +
202B ASN* 3.4 18.9 + - - +
203B PRO* 3.4 25.8 - - + +
355B PHE* 3.3 50.0 - - + -
356B LEU 3.4 4.7 - - - +
357B TRP* 4.0 16.2 - - + -
381B MET* 4.6 0.9 - - - +
382B LEU* 2.8 54.9 + - + +
387B PHE* 3.6 15.4 - - + -
398B LEU* 1.3 73.2 - - - +
400B ALA* 1.3 60.4 + - - +
401B SER 4.2 0.2 - - - +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.5 5.8 - - + -
333B ILE* 4.1 18.1 - - + +
355B PHE* 3.5 4.0 - - - -
356B LEU* 2.7 46.2 + - + +
358B ILE* 4.1 14.8 - - + -
381B MET* 3.5 27.6 - - + -
398B LEU* 3.8 0.6 + - + -
399B ARG* 1.3 73.3 - - - +
401B SER* 1.3 61.6 + - - +
402B PHE 3.8 0.3 + - - -
414B PHE* 4.6 0.2 - - + -
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 2.7 42.6 + - - +
38A GLY 3.3 27.0 + - - -
40A LEU 4.7 1.7 + - - -
333B ILE* 4.2 3.5 - - - +
354B MET* 3.4 11.1 + - - +
355B PHE* 3.9 12.0 - - - -
399B ARG* 4.1 0.8 + - - +
400B ALA* 1.3 72.2 - - - +
402B PHE* 1.3 62.5 + - - +
403B SER* 3.3 21.7 + - - -
404B SER 5.1 1.1 + - - -
405B ALA* 5.0 1.9 + - - +
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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