Contacts of the helix formed by residues 512 - 527 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A ILE* 5.0 16.4 - - + -
502A TYR* 6.3 2.0 - - + -
508A ASN* 4.3 11.9 - - - +
509A CYS* 3.1 23.6 - - - +
511A ASP* 1.3 80.5 - - - +
513A VAL* 1.3 65.9 + - + +
515A VAL* 2.8 26.4 + - - +
516A VAL* 2.9 22.6 + - + +
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Residues in contact with VAL 513 (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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509A CYS 4.1 13.0 - - - +
510A LEU* 3.1 24.3 + - + +
512A VAL* 1.3 80.9 - - + +
514A ILE* 1.3 65.2 + - - +
516A VAL* 2.8 23.0 + - + +
517A LEU* 2.9 37.0 + - + +
568A PHE* 5.2 18.4 - - + -
1006A PX6 5.4 9.9 - - + -
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Residues in contact with ILE 514 (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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227A TYR* 5.3 11.4 - - + -
230A PHE* 5.1 10.8 - - + -
491A GLU* 6.2 0.2 - - - +
510A LEU 4.0 4.1 + - - +
511A ASP* 3.1 29.4 - - - +
513A VAL* 1.3 74.2 - - - +
515A VAL* 1.3 66.6 + - + +
517A LEU* 4.2 5.4 - - - +
518A SER* 3.0 30.8 + - - +
565A THR* 4.7 11.2 - - - +
568A PHE* 5.1 13.9 - - + +
569A VAL* 3.9 35.7 - - + -
572A LYS* 5.6 14.1 - - + -
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Residues in contact with VAL 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 5.1 6.7 - - + -
487A TYR* 5.1 3.1 - - + +
488A VAL* 4.8 19.3 - - + -
491A GLU* 3.3 28.0 - - - +
511A ASP 4.3 4.0 - - - +
512A VAL* 2.8 14.8 + - - +
514A ILE* 1.3 83.5 - - + +
516A VAL* 1.3 70.7 + - + +
518A SER* 2.8 20.1 + - - +
519A VAL* 3.3 21.1 + - + +
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Residues in contact with VAL 516 (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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512A VAL* 2.9 26.1 + - + +
513A VAL* 2.8 18.7 + - + +
515A VAL* 1.3 79.4 - - + +
517A LEU* 1.3 72.6 + - + +
519A VAL* 3.9 4.3 + - - +
520A VAL* 3.3 22.7 + - + +
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Residues in contact with LEU 517 (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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513A VAL* 2.9 33.3 + - + +
514A ILE* 5.2 1.1 - - - +
516A VAL* 1.3 82.9 - - + +
518A SER* 1.3 69.1 + - - +
520A VAL* 2.8 27.0 + - + +
521A ALA* 3.0 5.9 + - - +
561A ILE* 4.4 22.4 - - + +
564A VAL* 4.5 20.2 - - + -
565A THR* 3.6 28.9 - - + +
568A PHE* 4.8 6.3 - - + -
1006A PX6 5.0 18.2 - - + -
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Residues in contact with SER 518 (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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480A PHE* 5.4 8.5 - - - -
484A ILE* 4.3 17.3 - - - +
514A ILE* 3.0 18.3 + - - -
515A VAL* 2.8 22.7 + - - -
517A LEU* 1.3 75.5 - - - +
519A VAL* 1.3 55.4 + - - +
521A ALA* 2.9 11.7 + - - +
522A ILE* 2.7 43.4 + - - +
565A THR* 4.2 12.1 - - - +
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Residues in contact with VAL 519 (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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484A ILE* 5.2 0.4 - - + -
488A VAL* 5.0 12.6 - - + -
515A VAL* 3.3 26.9 + - + +
516A VAL 4.2 3.1 - - - +
517A LEU 3.2 0.6 - - - -
518A SER* 1.3 84.6 + - - +
520A VAL* 1.3 58.1 + - + +
522A ILE* 2.7 39.6 + - + +
523A GLY 3.2 11.1 + - - +
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Residues in contact with VAL 520 (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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516A VAL* 3.3 21.3 - - + +
517A LEU* 2.8 22.0 + - + +
519A VAL* 1.3 74.6 - - + +
521A ALA* 1.3 60.2 + - - +
523A GLY 3.8 0.2 + - - -
524A ILE* 3.0 40.1 + - + +
561A ILE* 4.1 20.2 - - + -
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Residues in contact with ALA 521 (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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517A LEU 3.0 7.5 + - - +
518A SER* 2.9 14.0 + - - +
520A VAL* 1.3 76.4 - - - +
522A ILE* 1.3 68.3 + - + +
524A ILE* 3.2 24.4 - - - +
525A ASN* 3.1 14.8 + - - +
558A PHE* 3.8 21.3 - - + -
561A ILE* 4.8 16.9 - - + +
562A ALA* 5.1 4.0 - - + -
565A THR* 5.9 0.7 - - + -
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Residues in contact with ILE 522 (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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480A PHE* 5.0 13.5 - - + -
481A CYS* 4.6 26.0 - - + +
484A ILE* 4.4 23.1 - - + -
488A VAL* 5.9 0.9 - - + -
518A SER* 2.7 22.1 + - - +
519A VAL* 2.7 38.9 + - + +
521A ALA* 1.3 69.1 - - + +
523A GLY* 1.3 61.4 + - - +
525A ASN* 2.6 34.9 + - - +
526A ILE* 3.9 3.7 + - + +
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Residues in contact with GLY 523 (chain A).
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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519A VAL* 3.2 8.7 + - - +
520A VAL 4.5 0.2 - - - -
522A ILE* 1.3 83.5 - - - +
524A ILE* 1.3 57.7 + - - +
525A ASN 2.8 1.7 + - - -
526A ILE* 5.6 0.4 - - - -
527A TYR* 2.4 49.5 + - - -
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Residues in contact with ILE 524 (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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520A VAL* 3.0 35.7 - - + +
521A ALA* 3.2 19.1 - - - +
523A GLY* 1.3 72.5 - - - +
525A ASN* 1.3 61.5 + - - +
527A TYR* 4.7 0.7 - - + -
528A ARG* 3.0 50.3 - - + +
529A THR* 3.1 9.8 + - - +
554A TRP* 4.7 27.8 - - + -
557A GLN 5.4 0.9 - - - +
558A PHE* 4.0 28.3 - - + -
561A ILE* 4.8 5.4 - - + -
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Residues in contact with ASN 525 (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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464A ARG* 5.0 14.6 + - - +
477A GLU* 5.2 5.9 + - - -
521A ALA* 3.1 12.3 + - - +
522A ILE* 2.6 28.3 + - - +
523A GLY 2.8 1.2 + - - -
524A ILE* 1.3 81.3 - - - +
526A ILE* 1.3 97.6 + - - +
529A THR* 2.1 34.1 + - - +
530A SER* 3.1 5.2 + - - -
558A PHE* 4.3 25.6 - - + -
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Residues in contact with ILE 526 (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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464A ARG* 5.0 9.4 - - - +
477A GLU* 3.8 23.8 - - - +
478A ILE* 5.8 6.5 - - + -
481A CYS* 5.8 3.4 - - - -
522A ILE* 4.7 4.0 - - + +
523A GLY* 3.1 2.2 + - - +
525A ASN* 1.3 95.8 + - - +
527A TYR* 1.3 68.8 + - + +
530A SER* 2.2 52.7 + - - +
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Residues in contact with TYR 527 (chain A).
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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523A GLY* 2.4 41.8 + - - +
524A ILE* 5.6 0.4 - - + -
526A ILE* 1.3 75.9 - - + +
528A ARG* 1.3 94.9 + - + +
530A SER* 4.4 1.4 + - - -
531A ASN* 4.8 6.1 + - - +
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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