Contacts of the helix formed by residues 599 - 614 (chain A) 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 ASN 599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A TRP* 3.8 36.1 + - - +
205A ASP 3.2 16.8 - - - +
206A ASP* 4.8 0.4 - - - +
207A TRP* 3.6 4.0 - - - +
578A ARG* 3.5 27.4 - - - +
598A ALA* 1.3 76.1 - - - +
600A LYS* 1.3 65.3 + - - +
601A HIS* 3.2 4.7 + - - +
602A GLN* 2.8 54.7 + - - +
603A ALA* 3.0 21.1 + - - +
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Residues in contact with LYS 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.8 29.5 - - + +
203A ILE* 3.6 25.2 + - + +
205A ASP* 3.2 17.2 + - - +
206A ASP 3.5 18.4 - - - +
207A TRP* 3.6 45.1 - - + +
208A ASP* 5.0 10.7 + - - +
215A GLN* 5.4 2.8 + - - +
599A ASN* 1.3 75.6 - - - +
601A HIS* 1.3 64.1 + - - +
603A ALA* 3.3 2.8 + - - +
604A VAL* 3.1 29.1 + - - +
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Residues in contact with HIS 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL 5.4 1.6 - - - -
192A PHE* 3.4 29.5 - + - -
200A LEU 3.9 10.8 - - - +
201A PHE* 3.8 22.4 - + - -
202A GLY* 3.3 19.4 + - - -
203A ILE 3.0 24.6 + - - +
204A TRP* 4.1 17.9 - + + -
429A LYS* 6.1 2.8 - - - +
599A ASN* 3.2 4.2 + - - +
600A LYS* 1.3 74.2 - - - +
602A GLN* 1.3 72.2 + - + +
604A VAL 3.4 0.3 + - - -
605A THR* 3.1 35.8 + - - -
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Residues in contact with GLN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASP* 4.0 24.7 + - - -
308A ARG* 4.4 2.9 - - - +
429A LYS 4.9 9.2 - - - +
430A VAL* 4.7 4.6 - - - +
570A HIS* 5.5 0.5 - - - -
575A THR* 5.6 0.9 + - - -
576A LEU* 3.5 28.1 - - + +
578A ARG* 3.4 14.7 - - - +
598A ALA* 3.4 16.7 - - + -
599A ASN* 2.8 56.7 + - - +
601A HIS* 1.3 80.8 - - + +
603A ALA* 1.3 63.2 + - - +
605A THR* 3.3 9.4 + - - +
606A MET* 3.2 21.0 + - - +
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Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A TRP* 3.7 16.6 - - + +
213A PHE* 4.0 11.2 - - + -
216A LEU* 3.6 20.8 - - + +
570A HIS* 4.5 15.9 + - - +
598A ALA* 4.2 3.5 - - + +
599A ASN 3.0 17.5 + - - +
600A LYS 3.7 2.0 - - - +
602A GLN* 1.3 75.4 - - - +
604A VAL* 1.3 64.5 + - - +
606A MET* 3.3 5.0 + - - +
607A VAL* 3.2 25.1 + - - +
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Residues in contact with VAL 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE* 3.3 43.3 - - + -
195A LEU* 5.0 4.9 - - + -
197A LEU* 4.2 19.5 - - + -
200A LEU* 3.8 25.1 - - + -
216A LEU* 3.6 25.8 - - + -
600A LYS 3.1 17.2 + - - +
603A ALA* 1.3 73.0 - - - +
605A THR* 1.3 67.2 + - - +
607A VAL* 3.2 5.3 + - - +
608A SER* 2.9 21.8 + - - -
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Residues in contact with THR 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 4.0 29.1 - - + +
192A PHE* 3.8 8.3 - - - -
426A ALA* 5.2 0.4 - - - +
429A LYS* 4.1 20.4 - - + +
430A VAL* 3.4 22.7 - - + -
601A HIS* 3.1 31.5 + - - -
602A GLN* 3.4 12.6 - - - -
603A ALA 3.3 0.2 - - - -
604A VAL* 1.3 77.1 - - - +
606A MET* 1.3 61.3 + - - +
608A SER* 3.4 2.3 + - - -
609A VAL* 3.0 24.5 + - + +
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Residues in contact with MET 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A GLN* 3.8 21.8 - - + +
430A VAL* 3.9 26.9 - - + -
567A TYR* 3.8 26.0 - - + +
570A HIS* 4.7 12.1 - - + +
575A THR* 3.5 36.1 - - + +
602A GLN 3.2 9.1 + - - +
603A ALA 3.6 8.5 - - - +
604A VAL 3.2 0.8 - - - -
605A THR* 1.3 79.8 - - - +
607A VAL* 1.3 58.1 - - + +
609A VAL* 3.2 9.6 + - + -
610A VAL* 2.8 53.4 + - + +
613A LEU* 6.4 0.2 - - + -
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.0 16.6 - - + -
197A LEU* 5.4 1.3 - - + -
216A LEU* 3.8 37.5 - - + +
217A ILE* 5.3 2.0 - - + -
221A ILE* 4.1 18.4 - - + -
564A MET* 4.2 8.4 - - + +
567A TYR 5.0 6.5 - - - +
568A GLY* 4.3 16.2 - - - +
603A ALA 3.2 12.7 + - - +
604A VAL* 3.2 9.5 + - - +
606A MET* 1.3 74.9 - - + +
608A SER* 1.3 61.0 + - - +
610A VAL* 4.1 5.1 - - - +
611A ASN* 2.9 29.1 + - - +
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Residues in contact with SER 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU 5.2 1.4 + - - +
186A ARG 4.9 0.9 + - - -
187A VAL* 3.9 18.8 - - - +
191A ASP* 3.8 27.6 + - - +
192A PHE* 5.5 0.7 - - - -
195A LEU* 3.8 17.6 - - - +
604A VAL* 2.9 18.4 + - - -
605A THR 3.6 5.2 - - - -
607A VAL* 1.3 77.2 - - - +
609A VAL* 1.3 62.5 + - - +
611A ASN* 3.7 4.5 + - - +
612A ALA* 3.2 21.1 + - - +
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Residues in contact with VAL 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 5.4 6.3 - - + +
187A VAL* 3.9 16.8 - - + -
420A LEU* 5.4 2.2 - - + -
426A ALA* 3.8 32.5 - - + -
430A VAL* 4.8 6.3 - - + -
605A THR* 3.0 24.4 + - + +
606A MET* 3.2 18.1 + - + +
608A SER* 1.3 73.9 - - - +
610A VAL* 1.3 61.7 + - + +
612A ALA* 2.9 10.4 + - - +
613A LEU* 2.8 48.9 + - + +
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A GLN* 3.6 39.9 - - + +
564A MET* 3.6 22.7 - - + +
567A TYR* 4.0 18.4 - - + -
606A MET* 2.8 50.9 + - + +
607A VAL* 4.1 4.3 - - - +
609A VAL* 1.3 76.5 - - + +
611A ASN* 1.3 62.7 + - - +
613A LEU* 3.4 7.0 + - + +
614A THR* 3.1 24.7 + - + +
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Residues in contact with ASN 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 4.2 14.0 - - + +
220A ALA 4.6 6.0 + - - +
221A ILE* 3.8 25.7 - - + +
222A LYS 5.6 0.2 + - - -
564A MET* 3.7 15.0 - - + +
607A VAL 2.9 19.5 + - - +
608A SER* 3.7 7.6 + - - +
610A VAL* 1.3 78.1 - - - +
612A ALA* 1.3 62.9 + - - +
614A THR* 3.3 13.8 + - - -
615A THR* 3.6 10.3 + - - -
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Residues in contact with ALA 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.5 35.1 - - + +
185A PHE* 4.0 15.5 - - + -
608A SER 3.2 13.0 + - - +
609A VAL* 2.9 11.1 + - - +
611A ASN* 1.3 76.3 - - - +
613A LEU* 1.3 65.3 + - - +
614A THR 3.1 2.2 - - - -
615A THR* 2.7 27.8 + - - -
679A ILE* 3.8 6.1 - - - +
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Residues in contact with LEU 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PHE* 3.9 27.6 - - + -
369A GLN* 4.5 9.4 - - - +
373A HIS* 4.6 14.6 - - + -
378A HIS* 6.4 0.2 - - + -
420A LEU* 4.7 15.5 - - + -
560A ASN* 2.9 22.9 + - - +
563A GLN* 3.6 36.1 - - - +
606A MET* 6.4 0.2 - - + -
609A VAL* 2.8 40.1 + - + +
610A VAL* 3.4 6.9 + - + +
612A ALA* 1.3 72.1 - - - +
614A THR* 1.3 57.1 + - - +
615A THR 3.3 0.4 - - - -
679A ILE* 3.5 30.4 - - - +
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Residues in contact with THR 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A ASN 3.6 23.8 - - - +
561A PHE* 3.8 32.1 - - - +
563A GLN* 4.3 10.8 - - + +
564A MET* 4.4 12.0 - - + +
610A VAL* 3.1 22.7 + - + +
611A ASN* 3.3 13.2 + - - -
612A ALA 3.1 0.6 - - - -
613A LEU* 1.3 76.9 - - - +
615A THR* 1.3 62.8 + - - +
616A ILE* 3.3 6.4 + - - +
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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