Contacts of the helix formed by residues 569 - 573 (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 PHE 569 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B LEU 3.5 24.9 - - - -
211B GLU* 4.4 7.2 - - - -
213B PHE* 3.7 17.9 - - + -
214B ARG* 3.7 26.9 - - + -
217B ILE* 6.0 1.8 - - + -
225B LEU* 5.6 0.9 - - + -
226B PRO* 3.9 9.7 - - + +
228B ALA* 4.3 8.5 - - + -
229B ALA* 3.8 36.6 - - + +
232B TRP* 3.2 41.7 - + + -
565B ALA 5.4 0.2 + - - -
566B THR 4.0 5.0 + - - +
567B TYR 3.7 1.3 - - - -
568B GLY* 1.3 72.0 - - - +
570B HIS* 1.3 66.4 + - - +
571B PRO* 3.4 22.0 - - + -
572B ASN* 2.9 24.0 + - + +
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Residues in contact with HIS 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B PHE* 3.6 29.5 - + + +
216B LEU* 5.5 2.9 - - + +
567B TYR* 3.9 9.7 + - - +
568B GLY 3.6 4.6 + - - -
569B PHE* 1.3 71.9 - - - +
571B PRO* 1.3 75.0 - - + +
573B SER 2.9 28.1 + - - -
574B PRO* 3.2 14.5 - - + +
575B THR* 3.2 47.2 + - + +
576B LEU 4.6 1.4 + - - -
597B LEU* 4.9 3.8 - - + -
598B ALA* 3.7 32.0 + - + +
602B GLN 5.5 0.2 - - - -
603B ALA* 4.5 14.8 + - + -
606B MET* 4.7 10.8 - - + +
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Residues in contact with PRO 571 (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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210B LEU* 4.3 11.2 - - + +
213B PHE* 3.4 32.5 - - + -
232B TRP* 3.8 26.3 - - + -
358B LEU* 3.2 27.8 - - + +
361B ARG* 5.5 0.9 - - - +
569B PHE* 3.3 32.1 - - + -
570B HIS* 1.3 97.2 - - + +
572B ASN* 1.3 59.2 + - - +
573B SER 3.1 0.7 + - - -
574B PRO* 3.7 5.4 - - + +
597B LEU* 4.6 4.0 - - + -
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Residues in contact with ASN 572 (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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228B ALA* 3.6 22.1 - - + +
232B TRP* 3.8 14.9 - - + +
237B TRP* 2.8 28.6 + - - -
238B PHE* 5.9 0.7 - - - -
241B GLN* 3.3 23.7 + - - +
361B ARG* 3.1 25.8 + - - +
566B THR* 3.0 30.5 + - - +
569B PHE* 2.9 18.0 + - + +
571B PRO* 1.3 77.8 - - - +
573B SER* 1.3 58.2 + - - +
574B PRO* 4.0 0.7 - - - -
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Residues in contact with SER 573 (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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361B ARG* 3.3 26.5 + - - -
364B ASP* 5.0 1.7 + - - -
365B THR* 2.9 20.7 + - - -
566B THR* 3.8 11.5 + - - +
567B TYR* 3.3 37.0 + - - -
569B PHE 4.1 0.6 + - - -
570B HIS* 2.9 10.2 + - - +
571B PRO 3.1 0.2 - - - -
572B ASN* 1.3 82.8 - - - +
574B PRO* 1.3 71.1 - - - +
575B THR* 3.6 2.3 + - - +
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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