Contacts of the helix formed by residues 512 - 518 (chain H) in PDB entry 6K71
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 VAL 512 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408H LEU* 4.9 7.4 - - + -
409H LEU 4.0 8.7 - - - +
410H ALA 4.8 0.7 - - - -
411H ASN 4.1 2.5 - - - -
412H GLY* 3.5 31.4 - - - +
443H PHE* 5.0 10.9 - - + -
500H VAL* 4.4 21.8 - - + -
507H ILE* 4.3 13.5 - - + -
509H CYS 3.3 20.0 - - - +
510H SER 4.3 1.3 - - - +
511H SER* 1.3 71.5 - - - +
513H PRO* 1.3 72.5 - - + +
514H VAL 3.2 2.2 - - - -
515H VAL* 3.0 18.3 + - + +
516H LEU* 3.2 18.6 + - + +
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Residues in contact with PRO 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C ALA* 5.2 0.9 - - + +
335C TYR* 3.5 47.3 + - + -
410H ALA* 4.3 22.0 - - + +
510H SER 3.7 9.6 - - - +
511H SER* 3.6 4.3 - - - -
512H VAL* 1.3 95.0 - - + +
514H VAL* 1.3 57.9 + - - +
515H VAL 3.3 0.2 - - - -
516H LEU* 3.2 25.0 - - + +
517H ARG* 3.0 23.6 + - - +
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Residues in contact with VAL 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ASP* 3.2 49.6 - - + +
301B ILE* 6.3 2.2 - - + -
302B LYS* 6.5 0.9 - - + -
335C TYR* 4.3 14.3 - - + +
338C ARG* 5.5 6.7 - - + -
511H SER* 3.9 15.3 - - - +
513H PRO* 1.3 78.5 - - - +
515H VAL* 1.3 71.0 + - + +
517H ARG* 3.2 20.4 + - + +
518H VAL* 3.3 22.6 + - + +
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Residues in contact with VAL 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE* 4.9 8.7 - - + -
440H THR* 3.8 29.3 - - + +
443H PHE* 4.6 7.0 - - + -
502H THR* 4.9 2.2 - - + -
504H LEU* 4.7 20.0 - - + -
507H ILE* 3.7 37.5 - - + -
511H SER 4.0 9.2 - - - +
512H VAL* 3.0 12.1 + - + +
514H VAL* 1.3 81.7 - - + +
516H LEU* 1.3 61.6 + - - +
518H VAL* 3.4 19.5 - - + +
519H LYS* 5.0 6.3 + - - +
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Residues in contact with LEU 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408H LEU 4.9 3.4 - - - +
409H LEU 5.1 4.7 - - - +
410H ALA* 4.7 12.1 - - + +
443H PHE* 3.5 40.4 - - + -
444H CYS 3.6 26.7 - - - +
445H GLU* 4.9 3.4 - - - +
512H VAL* 3.2 32.9 + - + +
513H PRO* 3.2 22.4 - - + +
514H VAL 3.2 0.2 - - - -
515H VAL* 1.3 78.4 - - - +
517H ARG* 1.3 62.8 + - - +
518H VAL 3.3 0.5 + - - -
519H LYS* 4.0 6.6 + - - +
520H SER* 3.7 9.9 + - - -
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Residues in contact with ARG 517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TYR* 5.0 10.3 - - - +
338C ARG* 4.2 31.0 - - - +
513H PRO 3.0 12.3 + - - +
514H VAL* 3.2 20.3 + - + +
516H LEU* 1.3 76.7 - - - +
518H VAL* 1.3 64.7 + - + +
519H LYS 3.1 1.9 + - - -
520H SER* 3.2 22.6 + - - -
522H ASP* 2.6 37.3 + - - +
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Residues in contact with VAL 518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ILE 6.0 1.3 - - - +
302B LYS* 5.6 11.4 - - + +
304B TYR* 5.9 3.4 - - - +
504H LEU* 5.5 5.8 - - + -
514H VAL* 3.3 20.9 - - + +
515H VAL* 3.4 22.0 - - + +
516H LEU 3.3 0.4 - - - -
517H ARG* 1.3 80.6 - - + +
519H LYS* 1.3 78.2 + - + +
520H SER 3.4 3.9 + - - -
522H ASP* 4.5 18.1 + - - +
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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