Contacts of the helix formed by residues 539 - 553 (chain B) in PDB entry 2CVP
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 539 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A PHE* 3.9 19.1 - - + -
57A LYS* 4.2 1.6 - - - -
434A GLU* 3.8 11.0 + - - +
437A MET* 3.5 31.9 - - + +
538B HIS* 1.3 82.3 - - - +
540B SER* 1.3 58.9 + - - +
541B SER* 2.9 32.4 + - - -
542B THR* 2.7 28.4 + - - -
543B ASN* 3.0 22.9 + - - -
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Residues in contact with SER 540 (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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30A PHE* 3.5 15.6 + - - +
33A ASP 4.4 0.7 + - - -
34A PRO* 3.6 26.3 + - - -
36A ARG* 4.0 2.9 - - - +
37A PHE* 3.2 36.8 + - - +
539B ASP* 1.3 75.0 - - - +
541B SER* 1.3 53.4 + - - +
543B ASN* 3.8 9.9 - - - +
544B GLY* 2.8 27.7 + - - -
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Residues in contact with SER 541 (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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30A PHE* 3.7 10.4 - - - -
37A PHE* 3.7 10.7 - - - -
54A ASP* 2.6 22.0 + - - +
56A SER* 3.2 20.9 + - - -
57A LYS* 2.6 27.3 + - - +
539B ASP* 2.9 11.7 + - - -
540B SER* 1.3 78.1 + - - +
542B THR* 1.3 60.6 + - - +
544B GLY* 3.1 1.6 + - - -
545B LEU* 2.8 34.8 + - - +
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Residues in contact with THR 542 (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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57A LYS* 4.0 6.9 + - - -
430A LEU* 4.6 11.4 + - + +
434A GLU* 3.8 15.6 - - - +
525B ILE* 4.2 17.5 - - + -
538B HIS* 3.6 31.6 - - + +
539B ASP* 2.7 28.1 + - - -
541B SER* 1.3 75.1 + - - +
543B ASN* 1.3 63.6 + - - +
545B LEU* 3.3 11.4 + - - +
546B ILE* 3.0 36.9 + - + +
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Residues in contact with ASN 543 (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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535B VAL* 3.4 25.3 - - - +
536B THR* 3.3 19.3 + - + +
537B SER 3.6 0.7 + - - -
538B HIS* 2.8 48.4 + - - +
539B ASP 3.0 16.8 + - - +
540B SER* 3.8 7.9 - - - +
542B THR* 1.3 74.0 - - - +
544B GLY* 1.3 59.0 + - - +
546B ILE* 3.2 8.0 + - - +
547B SER* 2.9 33.1 + - - +
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Residues in contact with GLY 544 (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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37A PHE* 3.7 30.4 - - - -
540B SER 2.8 22.2 + - - -
541B SER 3.1 1.3 + - - -
543B ASN* 1.3 74.1 - - - +
545B LEU* 1.3 61.9 + - - +
547B SER* 3.4 8.7 + - - -
548B PHE* 3.1 21.7 + - - +
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Residues in contact with LEU 545 (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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52A LEU* 3.7 21.8 - - + -
54A ASP* 3.5 23.6 - - + +
57A LYS* 3.7 27.1 - - - +
429A PHE* 4.7 2.2 - - + -
430A LEU* 3.7 27.1 - - + -
433A THR* 4.8 2.7 - - - +
476A SER* 3.8 15.9 - - - +
478A VAL* 3.8 21.4 - - + +
541B SER 2.8 16.7 + - - +
542B THR* 3.8 3.1 - - - +
544B GLY* 1.3 73.9 - - - +
546B ILE* 1.3 61.2 + - - +
548B PHE* 3.3 7.3 + - - +
549B ILE* 3.0 34.4 + - + +
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Residues in contact with ILE 546 (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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430A LEU* 3.8 20.2 - - + -
525B ILE* 4.3 16.8 - - + -
528B GLU* 4.5 2.5 - - + +
529B LEU* 3.9 12.1 - - + -
535B VAL* 3.7 47.8 - - + +
538B HIS* 4.3 5.8 - - + -
542B THR* 3.0 35.4 + - + +
543B ASN* 3.2 5.1 + - - +
545B LEU* 1.3 73.5 - - - +
547B SER* 1.3 65.4 + - - +
549B ILE* 3.1 8.7 + - - +
550B LYS* 2.9 38.5 + - + +
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Residues in contact with SER 547 (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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534B ALA* 5.4 5.9 - - - +
535B VAL 5.0 8.7 + - - -
543B ASN* 2.9 16.9 + - - +
544B GLY* 3.6 11.7 - - - -
546B ILE* 1.3 78.2 - - - +
548B PHE* 1.3 57.0 + - - +
550B LYS* 3.3 7.5 + - - +
551B GLN* 2.9 32.0 + - - +
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Residues in contact with PHE 548 (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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43A ASN* 3.7 28.0 - - - -
50A HIS* 3.6 37.5 - + + -
52A LEU* 3.7 24.0 - - + -
410A VAL* 3.9 7.6 - - + -
478A VAL* 3.5 53.6 - - + -
479A PHE* 4.1 1.6 - - - -
480A THR 4.7 0.2 - - - -
544B GLY 3.1 13.1 + - - +
545B LEU 3.4 8.5 - - - +
546B ILE 3.3 0.2 - - - -
547B SER* 1.3 74.3 - - - +
549B ILE* 1.3 57.9 + - - +
551B GLN* 3.3 8.1 + - - -
552B GLN* 2.9 56.0 + - + +
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Residues in contact with ILE 549 (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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410A VAL* 3.4 26.6 - - + +
426A LEU* 3.8 32.5 - - + -
429A PHE* 5.7 2.2 - - + -
430A LEU* 4.0 28.0 - - + -
478A VAL* 4.6 9.9 - - + -
704A GOL 3.7 22.4 - - - +
529B LEU* 4.9 9.2 - - + -
545B LEU* 3.0 26.4 + - + +
546B ILE* 3.4 8.3 - - + +
548B PHE* 1.3 76.8 - - - +
550B LYS* 1.3 65.4 + - + +
553B ARG* 3.1 30.3 + - - +
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Residues in contact with LYS 550 (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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528B GLU 2.8 28.3 + - - -
529B LEU* 3.4 11.6 + - + +
530B GLU 3.5 5.5 + - - -
531B GLY 2.9 26.1 + - - +
532B SER* 4.2 9.4 - - - +
533B SER* 3.0 29.8 + - - +
534B ALA* 5.3 2.2 - - - -
535B VAL* 4.0 2.1 - - - +
546B ILE* 2.9 38.2 + - + +
547B SER* 3.8 6.1 - - - +
549B ILE* 1.3 77.2 - - + +
551B GLN* 1.3 61.8 + - - +
552B GLN 3.6 0.2 + - - -
553B ARG* 3.7 33.5 + - - +
554B ASP* 4.0 9.0 - - - +
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Residues in contact with GLN 551 (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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43A ASN* 5.2 4.9 + - - -
50A HIS* 5.2 3.6 - - - -
547B SER 2.9 18.1 + - - +
548B PHE* 3.8 9.4 - - - +
550B LYS* 1.3 79.4 - - - +
552B GLN* 1.3 86.8 + - - +
553B ARG 3.5 0.2 - - - -
554B ASP* 4.5 4.7 + - - +
555B THR* 3.8 9.9 + - - -
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Residues in contact with GLN 552 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLY* 4.9 0.3 - - - -
50A HIS* 3.7 31.5 + - - -
410A VAL* 3.9 18.6 - - + -
411A GLN* 2.9 22.3 + - - +
480A THR* 2.5 36.3 + - + +
548B PHE* 2.9 43.5 + - + +
549B ILE 3.3 0.2 + - - -
551B GLN* 1.3 102.1 + - - +
553B ARG* 1.3 60.8 + - - +
554B ASP 3.3 4.0 + - - -
555B THR* 3.4 20.4 + - - +
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Residues in contact with ARG 553 (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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410A VAL* 3.7 16.4 - - + +
411A GLN* 3.6 19.9 + - + +
704A GOL 2.8 56.4 + - - +
529B LEU* 2.8 23.8 + - - +
530B GLU* 4.8 0.8 - - - +
531B GLY* 2.6 39.1 + - - +
532B SER* 4.8 1.0 - - - +
549B ILE* 3.1 19.7 + - - +
550B LYS* 3.7 30.8 + - - +
551B GLN 3.5 0.4 - - - -
552B GLN* 1.3 77.2 - - - +
554B ASP* 1.3 73.9 + - - +
555B THR 3.6 0.2 - - - -
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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