Contacts of the helix formed by residues 593 - 608 (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 ASP 593 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B PHE* 3.1 37.2 - - - +
199B SER 3.3 18.8 - - - +
200B SER* 4.4 2.2 - - - +
201B TRP* 4.1 1.3 - - - -
572B ARG* 3.5 27.3 - - - +
592B PRO* 1.3 71.9 - - - +
594B ARG* 1.3 62.3 + - - +
595B GLY 3.2 2.3 + - - -
596B ARG* 2.7 55.3 + - - +
597B SER* 2.6 32.1 + - - -
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Residues in contact with ARG 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.9 50.0 - - + -
196B MET* 4.0 11.6 - - + +
199B SER* 2.9 41.5 + - - +
200B SER 3.3 10.7 + - - +
201B TRP* 3.7 38.8 - - + -
202B ASN* 3.4 26.1 + - - +
206B ASP* 3.0 21.8 + - - -
593B ASP* 1.3 72.3 - - - +
595B GLY* 1.3 65.1 + - - +
597B SER* 3.4 3.5 + - - -
598B CYS* 3.1 26.9 + - - -
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Residues in contact with GLY 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE 3.3 18.1 + - - -
194B MET 3.7 6.7 - - - -
196B MET 3.0 21.2 + - - -
197B PHE* 4.0 10.8 - - - -
593B ASP* 3.2 4.6 + - - -
594B ARG* 1.3 76.3 - - - +
596B ARG* 1.3 56.6 + - - +
598B CYS* 3.1 19.1 + - - +
599B TRP* 3.2 17.3 + - - -
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Residues in contact with ARG 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 3.3 32.8 + - + +
297B THR* 5.5 0.6 + - - -
298B ASP* 2.9 38.0 + - - +
301B THR* 3.5 21.3 + - - +
303B GLN* 3.7 16.4 - - - +
422B ASP 5.8 0.2 + - - -
423B LYS 2.8 28.3 + - - +
424B ALA* 3.5 19.6 - - + +
569B PRO* 4.8 0.6 - - + +
570B THR* 4.0 21.3 - - - -
572B ARG* 5.7 0.2 - - - +
592B PRO* 4.2 11.7 - - + -
593B ASP* 2.7 49.1 + - - +
595B GLY* 1.3 72.8 - - - +
597B SER* 1.3 60.2 + - - +
599B TRP* 4.6 1.3 - - - +
600B HIS* 3.0 29.8 + - - +
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Residues in contact with SER 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 3.0 29.5 + - - -
207B PHE* 4.7 1.6 - - - -
564B ILE* 3.4 28.0 - - - +
592B PRO* 3.5 11.2 + - - +
593B ASP 2.6 22.8 + - - -
594B ARG 3.5 5.6 - - - -
595B GLY 3.2 0.2 - - - -
596B ARG* 1.3 78.2 - - - +
598B CYS* 1.3 56.2 + - - +
600B HIS* 3.5 2.7 + - - +
601B LEU* 3.0 36.1 + - - +
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Residues in contact with CYS 598 (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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185B MET* 3.5 17.7 - - + +
190B ILE* 3.1 55.7 - - + +
193B PHE* 3.7 19.3 - - - -
194B MET* 4.2 11.9 - - - -
201B TRP* 5.6 1.6 - - - -
594B ARG 3.1 19.0 + - - -
595B GLY 3.1 10.0 + - - +
597B SER* 1.3 74.4 - - - +
599B TRP* 1.3 59.9 + - - +
601B LEU* 3.3 3.1 + - - +
602B GLY 3.0 24.4 + - - -
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Residues in contact with TRP 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL 6.0 0.9 - - - -
181B TYR* 4.5 16.9 - + + -
182B SER* 5.6 3.4 - - - -
185B MET* 3.5 36.1 - - + -
194B MET* 2.9 26.4 + - + +
195B HIS* 3.9 23.5 + + - -
197B PHE* 3.7 19.5 - + - -
420B LEU* 3.7 34.8 - - + +
423B LYS* 3.6 34.5 - - + -
424B ALA* 4.3 13.5 - - + -
595B GLY 3.2 24.2 + - - +
596B ARG* 3.6 4.0 + - - +
598B CYS* 1.3 79.3 - - - +
600B HIS* 1.3 56.6 + - - +
602B GLY* 4.0 0.2 - - - -
603B ALA* 3.0 30.1 + - - +
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Residues in contact with HIS 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 3.5 32.7 - + - -
424B ALA* 4.3 5.6 - - + +
561B ALA* 2.9 30.2 + - + +
564B ILE* 3.7 21.0 - - + +
567B ALA 3.6 17.6 + - - -
569B PRO* 3.5 27.5 - - + +
596B ARG 3.0 20.1 + - - +
597B SER* 3.6 5.2 - - - +
599B TRP* 1.3 74.9 - - - +
601B LEU* 1.3 70.6 + - + +
603B ALA* 3.2 5.9 + - - +
604B VAL* 3.0 38.1 + - + +
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Residues in contact with LEU 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.9 13.0 - - + +
190B ILE* 4.1 19.5 - - + -
201B TRP* 6.2 0.4 - - + -
207B PHE* 4.2 20.6 - - + -
210B ILE* 5.0 3.8 - - + -
211B PHE* 5.2 0.9 - - + -
214B ILE* 4.1 26.2 - - + -
558B TYR* 4.3 4.3 - - + -
562B SER* 3.3 44.0 - - - +
564B ILE* 4.6 4.3 - - + -
597B SER* 3.0 23.1 + - - +
598B CYS* 3.3 4.2 + - - +
600B HIS* 1.3 77.7 - - + +
602B GLY* 1.3 63.2 + - - +
604B VAL* 3.5 5.4 - - - +
605B TRP* 3.0 27.0 + - - +
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Residues in contact with GLY 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B TYR* 4.2 8.6 - - - -
184B ALA* 3.7 18.4 - - - +
185B MET* 4.0 17.9 - - - +
188B LEU* 4.3 4.2 - - - +
598B CYS 3.0 15.4 + - - -
599B TRP 4.0 0.9 - - - -
601B LEU* 1.3 76.6 - - - +
603B ALA* 1.3 62.3 + - - +
606B ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 603 (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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181B TYR* 3.5 34.7 - - + +
599B TRP 3.0 19.5 + - - +
600B HIS* 3.2 6.7 + - - +
602B GLY* 1.3 77.9 - - - +
604B VAL* 1.3 64.9 + - + +
606B ALA* 3.3 2.1 + - - +
607B LEU* 3.1 33.1 + - + +
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Residues in contact with VAL 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B PHE* 4.5 7.4 - - + -
363B GLN* 5.4 1.1 - - - +
557B GLN* 4.0 31.1 - - + +
558B TYR* 3.7 22.4 - - + +
561B ALA* 4.3 9.4 - - + -
562B SER* 4.5 11.2 - - - -
600B HIS* 3.0 46.9 + - + +
601B LEU* 3.5 11.9 - - - +
603B ALA* 1.3 78.6 - - + +
605B TRP* 1.3 62.4 + - - +
607B LEU* 4.4 2.9 - - - -
608B SER* 2.8 29.1 + - - -
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Residues in contact with TRP 605 (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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180B ASN 5.3 1.6 - - - -
183B LYS* 6.4 0.9 - - + -
184B ALA* 3.5 24.2 - - + -
187B ASN* 3.8 25.6 - - - -
188B LEU* 4.1 19.3 - - + +
558B TYR* 3.6 37.7 - + + -
601B LEU 3.0 18.8 + - - +
602B GLY 4.0 2.2 - - - +
604B VAL* 1.3 76.9 - - - +
606B ALA* 1.3 72.8 + - + +
608B SER* 3.1 7.6 + - - -
609B GLN* 2.8 64.5 + - + +
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Residues in contact with ALA 606 (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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180B ASN* 4.2 26.2 + - + +
181B TYR* 3.7 25.8 - - + -
602B GLY 3.0 19.7 + - - +
603B ALA 3.8 1.1 - - - +
605B TRP* 1.3 88.3 - - + +
607B LEU* 1.3 62.5 + - + +
608B SER 3.2 0.9 + - - -
609B GLN* 3.4 10.9 + - - +
673B ILE* 3.4 17.5 - - - +
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Residues in contact with LEU 607 (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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177B PHE* 3.9 18.4 - - + -
181B TYR* 3.7 26.0 - - + +
363B GLN* 5.2 5.6 - - - +
367B HIS* 4.6 11.2 - - + +
414B LEU* 5.8 3.4 - - + -
554B ASN* 2.9 26.5 + - - +
557B GLN* 3.8 34.5 - - - +
603B ALA* 3.1 23.7 + - + +
604B VAL* 4.5 1.8 - - + +
605B TRP 3.3 0.2 - - - -
606B ALA* 1.3 77.4 - - + +
608B SER* 1.3 59.0 + - - +
609B GLN 3.3 1.8 + - - -
673B ILE* 3.6 36.6 - - + +
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Residues in contact with SER 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B ASN* 3.7 4.6 + - - +
555B PHE* 3.5 33.3 - - - +
557B GLN* 3.5 12.1 + - - +
558B TYR* 3.4 24.0 + - - -
604B VAL 2.8 22.4 + - - -
605B TRP 3.1 7.6 + - - -
607B LEU* 1.3 76.9 - - - +
609B GLN* 1.3 65.9 + - - +
610B PHE* 3.9 6.8 + - - -
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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
------------------------------------------------------------
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