Contacts of the helix formed by residues 562 - 568 (chain B) in PDB entry 3VF1
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 SER 562 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLY 4.1 5.6 - - - -
246B SER* 2.7 23.7 + - - -
557B ALA 4.0 1.4 + - - -
558B ALA 2.6 28.6 + - - -
559B VAL* 4.0 1.6 - - - -
560B ASN 3.1 0.2 - - - -
561B PHE* 1.3 76.2 - - - +
563B GLN* 1.3 63.0 + - - +
564B MET 3.3 2.1 + - - -
565B ALA* 3.3 7.3 + - - +
566B THR* 3.2 21.7 + - - -
667B TRP* 3.6 38.6 - - - -
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Residues in contact with GLN 563 (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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246B SER* 3.9 5.6 - - - +
368B HIS* 3.5 17.0 - - + -
369B GLN* 2.9 33.6 + - - +
373B HIS* 4.6 5.0 + - - -
559B VAL 3.7 13.7 - - - +
560B ASN* 3.0 35.7 + - - +
561B PHE 3.2 1.4 - - - -
562B SER* 1.3 77.8 - - - +
564B MET* 1.3 56.9 + - - +
566B THR* 3.7 0.9 - - - -
567B TYR* 2.7 41.4 + - + +
610B VAL* 3.6 16.1 - - + +
613B LEU* 3.6 35.5 - - - +
614B THR* 4.3 1.8 - - + +
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Residues in contact with MET 564 (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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217B ILE* 4.8 5.2 - - - -
221B ILE* 4.1 23.6 - - + -
223B SER* 3.4 26.7 - - - +
224B GLY 5.4 0.4 - - - +
226B PRO* 3.6 8.9 - - + +
561B PHE 4.6 3.1 + - - +
562B SER 3.3 0.6 - - - -
563B GLN* 1.3 76.3 - - - +
565B ALA* 1.3 61.0 + - - +
566B THR 3.1 0.2 - - - -
568B GLY* 2.8 45.0 + - - -
607B VAL* 4.2 10.8 - - + +
610B VAL* 3.6 17.1 - - + +
611B ASN* 3.7 38.6 - - + +
614B THR* 4.4 12.5 - - + +
667B TRP* 6.2 1.3 - - + -
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Residues in contact with ALA 565 (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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226B PRO* 3.9 15.8 - - + +
227B HIS 6.0 0.9 - - - +
228B ALA* 3.9 22.2 + - - +
237B TRP* 5.2 2.1 - - - -
241B GLN* 5.0 2.2 - - - +
562B SER 3.3 9.5 + - - +
564B MET* 1.3 78.9 - - - +
566B THR* 1.3 60.9 + - - +
569B PHE 5.4 0.2 + - - -
572B ASN* 4.4 0.7 + - - -
667B TRP* 3.7 29.8 - - + +
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Residues in contact with THR 566 (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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241B GLN* 4.6 4.0 + - - +
245B GLY* 3.9 7.8 - - - -
246B SER* 2.8 39.3 + - - +
361B ARG* 4.0 13.7 - - - +
562B SER* 3.2 7.6 + - - -
563B GLN 3.9 2.9 - - - -
564B MET 3.1 0.4 - - - -
565B ALA* 1.3 80.9 - - - +
567B TYR* 1.3 79.7 + - + +
568B GLY 3.6 0.2 - - - -
569B PHE 4.0 1.3 + - - +
572B ASN* 3.0 32.8 + - - +
573B SER* 3.8 19.8 - - - +
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Residues in contact with TYR 567 (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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246B SER* 5.2 0.3 - - - -
364B ASP* 5.4 1.0 + - - -
365B THR* 3.5 29.7 + - + +
368B HIS* 2.8 41.5 + + - +
369B GLN* 3.5 20.1 + - - -
563B GLN* 2.7 36.5 + - + +
564B MET* 5.3 0.4 - - - -
566B THR* 1.3 85.0 - - + +
568B GLY* 1.3 68.0 + - - +
569B PHE 3.2 5.9 + - - -
570B HIS* 3.7 14.1 + - - +
573B SER* 3.3 39.8 + - - -
575B THR* 4.3 2.2 - - + -
606B MET* 3.8 24.2 - - + +
607B VAL* 5.0 5.9 - - - +
610B VAL* 4.0 15.9 - - + -
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Residues in contact with GLY 568 (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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213B PHE 4.9 5.2 - - - +
216B LEU* 5.0 2.3 - - - +
217B ILE* 3.9 17.2 - - - +
226B PRO* 3.8 10.1 - - - -
563B GLN 3.9 0.2 + - - -
564B MET* 2.8 42.6 + - - +
565B ALA 4.5 0.2 - - - -
566B THR 3.6 0.4 - - - -
567B TYR* 1.3 78.7 - - - +
569B PHE* 1.3 57.8 + - - +
570B HIS* 3.6 2.6 + - - +
607B VAL* 4.3 13.5 - - - +
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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