Contacts of the helix formed by residues 514 - 523 (chain B) in PDB entry 6MZL
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 ASP 514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463B ARG* 2.3 33.4 + - - +
513B LYS* 1.3 75.9 - - - +
515B ILE* 1.3 53.3 + - - +
516B GLN 3.3 3.1 - - - -
517B PRO* 3.2 25.5 - - + +
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Residues in contact with ILE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B ILE* 6.3 2.0 - - + -
463B ARG* 3.4 25.1 - - + +
464B ILE* 4.4 14.1 - - + -
504B LEU* 3.7 18.6 - - + -
507B ILE* 3.7 27.6 - - + -
508B SER* 3.5 25.4 - - - +
511B SER 4.9 2.2 - - - +
513B LYS* 2.8 25.8 + - + +
514B ASP* 1.3 72.3 - - - +
516B GLN* 1.3 65.4 + - + +
517B PRO 3.4 0.4 - - - -
518B LEU* 3.1 14.9 + - + +
519B ILE* 2.9 29.0 + - - +
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Residues in contact with GLN 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B LEU* 4.4 18.4 - - + +
508B SER* 4.9 7.7 + - - -
513B LYS 5.6 1.8 - - - +
515B ILE* 1.3 83.9 - - + +
517B PRO* 1.3 70.0 - - + +
519B ILE* 3.3 21.8 + - + +
520B LYS* 2.9 41.6 + - + +
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Residues in contact with PRO 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ARG* 4.0 8.7 - - - +
514B ASP* 3.2 35.0 - - + +
516B GLN* 1.3 85.3 - - + +
518B LEU* 1.3 58.1 + - - +
520B LYS* 4.4 4.7 - - + +
521B GLN* 2.9 41.1 + - - +
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B VAL* 5.1 6.5 - - + +
459B LEU* 3.8 32.5 - - + +
460B ILE* 3.7 31.9 - - + -
463B ARG* 3.1 41.9 - - - +
515B ILE* 3.1 19.8 + - + +
517B PRO* 1.3 74.9 - - - +
519B ILE* 1.3 58.7 + - + +
521B GLN* 4.5 2.2 - - - -
522B TRP* 2.9 57.5 + - + +
523B VAL* 3.8 1.8 + - + +
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Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B TRP* 5.7 4.7 - - + -
416B PRO* 6.2 0.4 - - + -
500B THR* 6.4 1.8 - - + -
504B LEU* 3.7 41.1 - - + -
515B ILE 2.9 20.0 + - - +
516B GLN* 3.4 16.6 - - + +
518B LEU* 1.3 76.1 - - + +
520B LYS* 1.3 62.4 + - + +
522B TRP 3.0 0.2 + - - -
523B VAL* 2.7 51.3 + - + -
524B ASP* 2.7 34.6 + - - +
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Residues in contact with LYS 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B GLN* 2.9 27.0 + - - +
517B PRO* 4.3 3.8 - - + +
519B ILE* 1.3 83.9 - - + +
521B GLN* 1.3 63.3 + - - +
524B ASP* 3.6 19.3 - - + +
525B GLN* 3.5 14.9 - - - +
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Residues in contact with GLN 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B ARG* 4.1 16.6 + - - +
517B PRO* 2.9 27.0 + - + +
518B LEU* 4.5 0.3 - - - +
520B LYS* 1.3 75.9 - - - +
522B TRP* 1.3 85.4 + - + +
525B GLN* 2.9 17.4 + - - +
559B LYS* 2.4 31.4 + - - +
560B TYR 5.7 0.2 + - - -
561B VAL* 3.8 33.0 - - + +
562B GLY 5.1 2.0 - - - +
563B PRO* 5.2 7.9 - - - +
564B LEU* 5.6 2.8 - - - +
582B GLU* 5.4 1.6 + - - -
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Residues in contact with TRP 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 5.1 0.3 - - - +
452B LYS* 3.8 24.2 + - - -
456B VAL* 4.2 23.1 - - + +
459B LEU* 3.5 19.1 - - + +
518B LEU* 2.9 39.7 + - + +
521B GLN* 1.3 93.9 + - + +
523B VAL* 1.3 68.3 + - - +
524B ASP 3.3 0.9 - - - -
525B GLN 4.1 5.4 + - - +
527B GLY 3.4 21.8 - - - -
529B VAL* 3.7 15.9 - - + -
559B LYS* 3.3 16.2 - - - +
561B VAL* 3.7 16.6 - - + -
636B VAL* 3.6 42.8 - - + +
637B LEU* 3.6 32.1 - - + -
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TRP* 3.7 42.4 - - + +
413B LEU* 3.4 3.6 - - - +
414B LEU* 3.3 50.8 + - + +
416B PRO* 5.3 1.6 - - + -
456B VAL* 4.1 19.3 - - + -
500B THR* 5.9 0.2 - - + -
518B LEU* 4.6 2.9 - - + +
519B ILE* 2.7 41.4 + - + +
522B TRP* 1.3 74.4 - - - +
524B ASP* 1.3 66.9 + - - +
525B GLN 3.7 0.2 - - - -
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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