Contacts of the helix formed by residues 512 - 527 (chain C) in PDB entry 5MKF
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495C ILE* 5.0 16.8 - - + -
502C TYR* 6.3 1.8 - - + -
508C ASN* 4.3 12.1 - - - +
509C CYS* 3.1 23.3 - - - +
511C ASP* 1.3 81.6 - - + +
513C VAL* 1.3 65.7 + - + +
515C VAL* 2.8 26.3 + - - +
516C VAL* 2.9 20.9 + - + +
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Residues in contact with VAL 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509C CYS 4.1 13.2 - - - +
510C LEU* 3.1 25.7 + - + +
512C VAL* 1.3 79.1 - - + +
514C ILE* 1.3 65.7 + - - +
516C VAL* 2.8 21.2 + - + +
517C LEU* 2.9 37.2 + - + +
568C PHE* 5.2 18.8 - - + -
1006C PX6 5.4 9.4 - - + -
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Residues in contact with ILE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C TYR* 5.3 11.4 - - + -
230C PHE* 5.1 10.5 - - + -
510C LEU 4.0 4.1 + - - +
511C ASP* 3.1 29.6 - - - +
513C VAL* 1.3 74.4 - - - +
515C VAL* 1.3 65.7 + - + +
517C LEU* 3.7 5.0 + - - +
518C SER* 3.0 31.2 + - - +
565C THR* 4.7 10.8 - - - +
568C PHE* 5.1 14.6 - - + +
569C VAL* 3.9 37.5 - - + +
572C LYS* 5.6 14.4 - - + -
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Residues in contact with VAL 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ILE* 5.1 7.0 - - + -
487C TYR* 5.1 2.7 - - + +
488C VAL* 4.8 19.3 - - + +
491C GLU* 3.3 29.4 - - - +
511C ASP 4.3 3.8 - - - +
512C VAL* 2.8 14.3 + - - +
514C ILE* 1.3 83.3 - - + +
516C VAL* 1.3 71.8 + - + +
518C SER* 2.8 19.5 + - - +
519C VAL* 3.3 21.3 + - + +
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Residues in contact with VAL 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C VAL* 2.9 25.7 + - + +
513C VAL* 2.8 19.3 + - + +
515C VAL* 1.3 79.3 - - + +
517C LEU* 1.3 71.0 + - + +
519C VAL* 3.9 3.6 + - - +
520C VAL* 3.3 23.2 + - + +
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C VAL* 2.9 33.4 + - + +
514C ILE* 4.2 1.1 - - - +
516C VAL* 1.3 83.5 - - + +
518C SER* 1.3 69.1 + - - +
520C VAL* 2.8 27.6 + - + +
521C ALA* 3.0 6.1 + - - +
561C ILE* 4.4 23.0 - - + +
564C VAL* 4.5 20.9 - - + -
565C THR* 3.6 27.6 - - + +
568C PHE* 4.8 6.3 - - + -
1006C PX6 5.0 19.1 - - + -
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Residues in contact with SER 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C PHE* 5.4 9.2 - - - -
484C ILE* 4.3 17.7 - - - +
514C ILE* 3.0 18.4 + - - -
515C VAL* 2.8 23.0 + - - -
517C LEU* 1.3 76.6 - - - +
519C VAL* 1.3 57.1 + - - +
521C ALA* 2.9 11.7 + - - +
522C ILE* 2.7 42.9 + - - +
565C THR* 4.2 11.8 - - - +
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Residues in contact with VAL 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C ILE* 5.2 0.4 - - + -
488C VAL* 5.0 12.6 - - + -
515C VAL* 3.3 26.6 + - + +
516C VAL* 4.2 4.0 - - - +
517C LEU 3.2 0.4 - - - -
518C SER* 1.3 84.1 + - - +
520C VAL* 1.3 57.9 + - + +
522C ILE* 2.7 39.9 + - + +
523C GLY* 3.2 11.4 + - - +
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Residues in contact with VAL 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C VAL* 3.3 21.3 - - + +
517C LEU* 2.8 20.9 + - + +
519C VAL* 1.3 75.1 - - + +
521C ALA* 1.3 60.6 + - - +
523C GLY* 3.8 0.3 + - - -
524C ILE* 3.0 40.8 + - + +
561C ILE* 4.1 21.1 - - + -
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Residues in contact with ALA 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LEU 3.0 6.4 + - - +
518C SER* 2.9 15.5 + - - +
520C VAL* 1.3 77.3 - - - +
522C ILE* 1.3 67.4 + - + +
524C ILE* 3.2 24.7 - - - +
525C ASN* 3.1 14.7 + - - +
558C PHE* 3.8 21.3 - - + -
561C ILE* 4.8 16.1 - - + +
562C ALA* 5.1 4.0 - - - -
565C THR* 5.9 0.9 - - + -
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Residues in contact with ILE 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480C PHE* 5.0 13.5 - - + -
481C CYS* 4.6 26.7 - - + +
484C ILE* 4.4 22.2 - - + -
488C VAL* 5.9 0.7 - - + -
518C SER* 2.7 22.2 + - - +
519C VAL* 2.7 41.0 + - + +
521C ALA* 1.3 69.8 - - + +
523C GLY* 1.3 61.8 + - - +
525C ASN* 2.6 34.6 + - - +
526C ILE* 4.7 4.5 - - + +
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Residues in contact with GLY 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C VAL* 3.2 8.2 + - - +
520C VAL 4.5 0.2 - - - -
522C ILE* 1.3 83.9 - - - +
524C ILE* 1.3 57.9 + - - +
525C ASN 2.8 1.9 + - - -
526C ILE* 5.6 1.1 - - - -
527C TYR* 2.4 50.2 + - - -
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Residues in contact with ILE 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C VAL* 3.0 35.7 - - + +
521C ALA* 3.2 19.1 - - - +
523C GLY* 1.3 72.2 - - - +
525C ASN* 1.3 61.7 + - - +
527C TYR* 4.7 1.1 - - + -
528C ARG* 3.0 51.7 - - + +
529C THR* 3.1 9.4 + - - +
554C TRP* 4.7 27.8 - - + -
557C GLN 5.4 1.1 - - - +
558C PHE* 4.0 28.3 - - + -
561C ILE* 4.8 4.3 - - + -
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Residues in contact with ASN 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C ARG* 5.0 15.6 + - - +
477C GLU* 5.2 5.9 + - - +
521C ALA 3.1 12.5 + - - +
522C ILE* 2.6 28.8 + - - +
523C GLY 2.8 1.6 + - - -
524C ILE* 1.3 80.7 - - - +
526C ILE* 1.3 98.4 + - - +
529C THR* 2.1 34.3 + - - +
530C SER* 3.1 4.7 + - - -
558C PHE* 4.3 24.5 - - + -
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Residues in contact with ILE 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C ARG* 5.0 9.6 - - - +
477C GLU* 3.8 24.5 - - - +
478C ILE* 5.8 6.7 - - + -
481C CYS* 5.8 2.9 - - - -
522C ILE* 4.7 3.4 - - + +
523C GLY* 3.1 1.8 + - - +
525C ASN* 1.3 95.8 + - - +
527C TYR* 1.3 68.4 + - + +
530C SER* 2.2 54.0 + - - +
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Residues in contact with TYR 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C GLY* 2.4 42.5 + - - +
524C ILE* 6.3 0.2 - - + -
526C ILE* 1.3 75.8 - - - +
528C ARG* 1.3 94.7 + - + +
530C SER* 4.4 1.6 + - - -
531C ASN* 4.8 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
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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