Contacts of the helix formed by residues 556 - 562 (chain B) in PDB entry 3V98
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 556 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ALA* 3.8 9.9 - - - +
551B ALA 4.8 0.2 + - - -
552B ALA 4.9 1.6 + - - -
553B VAL 5.0 0.6 - - - -
554B ASN 3.2 2.6 - - - +
555B PHE* 1.3 77.2 - - - +
557B GLN* 1.3 64.6 + - - +
558B TYR 3.4 2.2 - - - -
559B ASP* 3.5 3.8 - - - +
560B TRP* 3.1 30.7 + - - +
661B TYR* 3.3 35.8 - - - -
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Residues in contact with GLN 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA* 4.7 4.3 - - + -
359B PHE* 5.9 1.6 - - + -
362B HIS* 3.6 22.4 - - + +
363B GLN* 2.7 30.2 + - - +
367B HIS* 4.0 6.8 - - - -
553B VAL 4.2 0.7 - - - +
554B ASN* 3.1 43.5 + - - +
555B PHE 3.4 1.2 - - - -
556B GLY* 1.3 78.0 - - - +
558B TYR* 1.3 58.7 + - - +
561B ALA* 2.8 36.8 + - + +
562B SER 3.9 0.2 + - - -
604B VAL* 4.0 20.7 - - + +
607B LEU* 3.8 27.1 - - - +
608B SER* 3.5 7.4 + - - +
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Residues in contact with TYR 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.2 6.2 - - + +
211B PHE* 5.4 0.2 - - - -
214B ILE* 2.6 49.1 + - - +
215B SER* 4.7 0.6 - - - -
216B ASN* 3.6 28.7 - - + +
219B SER* 4.5 2.5 - - - -
555B PHE 5.1 0.2 + - - -
556B GLY 3.4 0.2 - - - -
557B GLN* 1.3 75.2 - - - +
559B ASP* 1.3 65.3 + - - +
562B SER* 2.6 58.4 + - - -
601B LEU* 4.3 11.7 - - + -
604B VAL* 3.7 17.7 + - + +
605B TRP* 3.6 50.5 - + + -
608B SER* 3.4 13.9 + - - +
609B GLN* 5.9 0.7 - - - +
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Residues in contact with ASP 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN* 2.9 31.0 + - - -
218B ILE* 3.6 26.1 - - + +
219B SER* 3.2 25.8 + - - -
222B VAL* 3.9 2.8 - - - +
555B PHE 4.1 5.2 - - - +
556B GLY* 3.5 7.0 - - - +
558B TYR* 1.3 81.1 - - - +
560B TRP* 1.3 59.8 + - + +
563B TRP 5.4 0.3 + - - -
660B TYR* 3.4 13.9 + - - -
661B TYR* 2.7 41.0 + - - +
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Residues in contact with TRP 560 (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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218B ILE* 4.0 12.6 - - + +
222B VAL* 3.6 30.2 - - + +
231B MET* 4.0 13.0 - - + -
234B TYR* 3.9 28.3 - + - -
235B GLN* 3.3 42.4 - - + +
238B ASN 4.1 6.4 + - - -
239B GLY* 3.9 11.1 - - - -
240B ALA* 3.9 25.8 - - + +
355B ARG* 5.4 2.9 - - - +
556B GLY 3.1 16.1 + - - +
559B ASP* 1.3 79.1 - - + +
561B ALA* 1.3 61.8 + - + +
562B SER 3.7 0.4 - - - -
563B TRP 4.5 1.9 - - - +
566B ASN* 2.8 32.8 + - - +
567B ALA* 4.2 2.5 - - - +
657B LEU* 3.9 30.1 - - + -
661B TYR* 3.2 32.5 + + - -
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Residues in contact with ALA 561 (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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359B PHE* 4.1 15.3 - - + -
557B GLN* 2.8 19.9 + - - +
560B TRP* 1.3 76.0 - - + +
562B SER* 1.3 65.3 + - - +
563B TRP 3.2 10.0 + - - +
564B ILE* 3.9 1.4 + - - -
567B ALA* 3.6 23.0 - - + +
600B HIS* 2.9 33.5 + - + +
604B VAL* 4.3 5.6 - - + -
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Residues in contact with SER 562 (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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207B PHE* 3.8 3.3 - - - -
211B PHE* 3.6 13.9 - - - -
219B SER* 3.0 24.9 + - - -
557B GLN 3.9 1.2 + - - -
558B TYR* 2.6 56.5 + - - +
561B ALA* 1.3 78.1 - - - +
563B TRP* 1.3 55.7 + - - +
564B ILE* 3.1 10.9 + - - +
601B LEU* 3.3 26.4 - - - +
604B VAL* 4.5 4.2 - - - +
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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