Contacts of the strand formed by residues 504 - 510 (chain A) in PDB entry 2VKX
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 SER 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A SER* 3.8 5.4 + - - -
503A PRO* 1.3 73.0 + - - +
505A ILE* 1.3 64.1 + - - +
506A ASP* 3.6 4.4 + - - +
519A PHE* 3.1 6.5 - - - +
520A ASP* 2.9 51.0 + - - -
521A GLU 4.9 0.8 + - - -
588A SER* 5.0 0.4 - - - -
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Residues in contact with ILE 505 (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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503A PRO 4.2 0.4 + - - -
504A SER* 1.3 76.1 - - - +
506A ASP* 1.3 64.3 + - - +
507A GLN 3.7 9.6 - - - +
508A VAL* 3.7 26.9 - - + -
517A VAL* 4.3 10.8 - - + -
518A GLN 3.8 4.5 - - - +
519A PHE* 4.3 0.4 - - - -
574A VAL* 3.7 26.9 - - + +
575A ARG* 4.2 5.6 - - - -
576A LEU* 4.3 16.8 - - + +
588A SER* 3.8 24.1 - - - +
589A ALA 4.0 4.9 - - - +
591A SER* 3.8 18.6 - - - +
623B LYS* 5.6 2.9 - - - -
654B GLY* 3.2 24.8 - - - +
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Residues in contact with ASP 506 (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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504A SER* 4.1 6.0 - - - +
505A ILE* 1.3 81.4 - - - +
507A GLN* 1.3 63.4 + - + +
518A GLN* 2.8 25.0 + - - +
519A PHE 4.0 2.4 + - - -
520A ASP* 2.6 46.0 + - - +
623B LYS* 5.9 0.7 - - - -
653B SER* 2.8 44.6 + - - +
654B GLY* 4.4 2.9 + - - -
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Residues in contact with GLN 507 (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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505A ILE* 3.7 1.4 - - - +
506A ASP* 1.3 89.4 + - + +
508A VAL* 1.3 74.5 + - - +
509A GLU* 4.1 3.4 - - + +
516A GLN 5.2 0.4 - - - +
517A VAL* 3.5 1.9 - - - -
518A GLN* 2.9 69.0 + - + +
623B LYS* 5.5 2.0 - - - +
626B ASP* 4.1 13.5 + - - +
630B PRO* 3.4 12.0 - - + +
631B ILE* 2.9 54.9 + - - +
653B SER* 3.6 5.4 + - - -
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Residues in contact with VAL 508 (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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505A ILE* 3.7 13.5 - - + -
507A GLN* 1.3 85.4 + - - +
509A GLU* 1.3 60.9 + - - +
510A PRO* 3.0 13.9 - - - +
515A ALA* 4.8 4.3 - - + -
516A GLN 3.3 7.2 - - - +
517A VAL* 4.4 14.4 - - + -
574A VAL* 4.4 2.7 - - + -
591A SER* 3.4 26.2 - - - +
593A PHE* 3.5 41.5 - - + -
623B LYS* 4.1 24.6 - - + +
624B GLN 4.7 2.3 - - - +
626B ASP* 5.2 2.8 - - - +
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Residues in contact with GLU 509 (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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507A GLN* 4.1 2.7 - - + +
508A VAL* 1.3 71.3 - - - +
510A PRO* 1.3 62.5 - - - +
511A TYR* 3.3 46.4 + - + +
515A ALA* 3.5 1.3 - - - -
516A GLN* 2.9 45.1 + - + +
625B ASP* 2.6 29.9 - - - +
626B ASP* 2.9 47.6 + - - +
628B GLY* 4.0 4.7 + - - -
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Residues in contact with PRO 510 (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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508A VAL* 3.0 14.1 - - + +
509A GLU* 1.3 97.1 - - - +
511A TYR* 1.3 64.7 + - - +
514A THR 4.2 4.0 - - - +
515A ALA* 4.4 4.3 - - + -
593A PHE* 4.1 21.8 - - + -
594A LYS 3.5 25.6 - - - +
595A THR* 4.3 2.9 - - - -
596A GLN* 2.9 24.5 + - + +
623B LYS 4.5 2.7 - - - +
624B GLN* 3.7 15.5 - - - +
625B ASP 3.6 16.2 - - - +
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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