Contacts of the helix formed by residues 519 - 533 (chain T) in PDB entry 5MQF
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 LYS 519 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518T LYS* 1.3 73.0 - - - +
520T GLU* 1.3 59.7 + - - +
521T TYR 3.0 4.3 - - - -
522T MET* 3.5 4.6 + - - +
523T GLU* 2.9 29.8 + - - +
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Residues in contact with GLU 520 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483T GLU* 6.4 2.0 - - + -
486T THR* 5.8 7.4 - - - -
518T LYS* 3.5 4.3 - - + +
519T LYS* 1.3 78.0 - - - +
521T TYR* 1.3 56.7 + - - +
523T GLU* 3.9 8.8 - - - +
524T SER* 2.9 28.8 + - - -
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Residues in contact with TYR 521 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514T PHE 3.2 27.4 - - - +
515T CYS* 3.4 11.8 - - - +
517T LEU* 4.8 0.9 - - + -
518T LYS* 3.4 21.4 + - + +
519T LYS 3.0 0.8 - - - -
520T GLU* 1.3 74.7 - - - +
522T MET* 1.3 62.8 + - - +
524T SER* 2.9 9.9 + - - -
525T PHE* 2.9 25.8 + - - +
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Residues in contact with MET 522 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515T CYS* 2.8 29.3 + - - +
516T MET* 5.3 1.1 - - - -
518T LYS 3.4 5.8 + - - +
519T LYS* 4.2 5.4 - - - +
521T TYR* 1.3 72.6 - - - +
523T GLU* 1.3 57.2 + - - +
525T PHE* 3.1 4.6 + - - +
526T GLU* 2.9 27.4 + - - +
560T LEU* 4.1 24.7 - - + +
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Residues in contact with GLU 523 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519T LYS 2.9 20.5 + - - +
520T GLU* 3.9 9.4 - - - +
522T MET* 1.3 78.1 - - - +
524T SER* 1.3 55.8 + - - +
526T GLU* 3.1 7.5 + - - +
527T GLY* 2.9 26.9 + - - -
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Residues in contact with SER 524 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486T THR* 4.9 11.0 - - - -
487T LYS* 5.0 9.4 - - - -
490T CYS* 4.5 19.1 - - - +
520T GLU 2.9 20.9 + - - -
521T TYR* 2.9 7.6 + - - -
523T GLU* 1.3 76.0 - - - +
525T PHE* 1.3 49.9 + - - +
527T GLY* 4.6 1.1 - - - +
528T ILE* 2.7 40.2 + - - +
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Residues in contact with PHE 525 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490T CYS* 6.0 0.9 - - - -
515T CYS* 3.7 28.3 - - + -
521T TYR 2.9 5.4 + - - +
522T MET 3.1 8.7 + - - +
524T SER* 1.3 76.8 - - - +
526T GLU* 1.3 59.7 + - - +
528T ILE* 4.3 3.3 - - - +
529T PHE* 2.9 30.0 + - - +
560T LEU* 4.1 11.7 - - + -
561T PRO* 5.4 5.6 - - + +
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Residues in contact with GLU 526 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522T MET 2.9 12.7 + - - +
523T GLU* 3.1 10.3 + - - +
525T PHE* 1.3 75.4 - - - +
527T GLY* 1.3 59.9 + - - +
529T PHE* 3.3 5.2 + - - +
530T LYS* 2.9 27.0 + - - +
560T LEU 4.8 8.5 + - - +
561T PRO* 5.4 3.8 - - - -
562T TRP* 5.2 11.2 - - + +
563T SER* 5.8 2.7 - - - +
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Residues in contact with GLY 527 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523T GLU 2.9 14.3 + - - -
524T SER* 4.8 0.7 - - - -
526T GLU* 1.3 73.6 - - - +
528T ILE* 1.3 59.8 + - - +
530T LYS* 3.2 8.1 + - - +
531T GLU* 2.9 28.3 + - - +
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Residues in contact with ILE 528 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487T LYS 5.8 0.7 - - - +
490T CYS* 4.6 19.5 - - + +
491T ASN* 5.3 5.6 - - + +
524T SER 2.7 24.2 + - - +
525T PHE* 4.3 3.8 - - - +
527T GLY* 1.3 76.1 - - - +
529T PHE* 1.3 57.8 + - - +
531T GLU* 3.4 7.6 + - - +
532T GLN* 2.9 26.9 + - - +
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Residues in contact with PHE 529 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525T PHE 2.9 21.4 + - - +
526T GLU* 3.7 6.1 - - - +
528T ILE* 1.3 75.2 - - - +
530T LYS* 1.3 59.1 + - - +
532T GLN* 3.1 9.1 + - - +
533T TYR* 2.9 27.7 + - - +
561T PRO* 5.8 6.1 - - + -
564T VAL* 4.8 19.3 - - + -
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Residues in contact with LYS 530 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526T GLU 2.9 14.0 + - - +
527T GLY* 3.5 11.7 - - - +
529T PHE* 1.3 78.6 - - - +
531T GLU* 1.3 60.8 + - - +
533T TYR* 3.3 16.6 + - - +
534T ASP* 3.5 9.9 + - - +
567T CYS* 5.4 9.2 - - + -
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Residues in contact with GLU 531 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527T GLY 2.9 15.6 + - - +
528T ILE* 3.7 8.1 - - - +
530T LYS* 1.3 75.2 - - - +
532T GLN* 1.3 62.3 + - - +
534T ASP* 3.3 19.6 + - - +
535T THR* 3.9 3.6 + - - -
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Residues in contact with GLN 532 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528T ILE 2.9 17.2 + - - +
529T PHE* 3.1 10.9 + - - +
531T GLU* 1.3 75.0 - - - +
533T TYR* 1.3 63.1 + - - +
534T ASP 3.1 0.4 - - - -
535T THR* 3.2 22.4 + - - +
536T ILE 4.5 1.2 + - - -
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Residues in contact with TYR 533 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529T PHE 2.9 12.7 + - - +
530T LYS* 3.6 12.6 - - - +
531T GLU 3.3 0.6 - - - -
532T GLN* 1.3 75.7 - - - +
534T ASP* 1.3 57.0 + - - +
535T THR 3.2 1.8 + - - -
536T ILE* 4.4 9.6 + - - +
567T CYS* 4.5 25.8 - - + +
568T ILE* 6.1 0.7 - - - -
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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