Contacts of the helix formed by residues 518 - 527 (chain C) in PDB entry 6DBU
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 PRO 518 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C TYR* 3.8 25.6 - - + +
514C GLN* 3.5 27.6 - - - +
516C PHE 4.0 1.6 - - - +
517C GLN* 1.3 94.0 - - + +
519C LEU* 1.3 68.5 + - - +
520C HIS* 3.6 7.4 - - + +
521C THR* 3.2 17.2 - - + +
522C LEU* 3.2 19.4 + - - +
7H T 4.4 23.1 - - - +
8H G 3.8 11.7 - - - +
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Residues in contact with LEU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C ARG* 4.6 16.4 - - - +
497C CYS* 4.5 13.5 - - + +
500C TYR* 3.4 35.9 - - + -
501C HIS* 3.7 34.3 - - + +
504C TYR* 5.1 2.7 - - + -
518C PRO* 1.3 75.5 - - + +
520C HIS* 1.3 67.7 + - - +
522C LEU* 2.9 19.2 + - + +
523C ARG* 3.0 28.3 + - + +
9H T 6.1 5.8 - - + -
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Residues in contact with HIS 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C PRO* 4.8 9.9 - - + +
519C LEU* 1.3 79.4 - - - +
521C THR* 1.3 78.0 + - - +
523C ARG* 3.4 25.9 + - - +
524C ASN* 2.9 30.2 + - + +
6H C 4.9 1.8 - - - -
7H T 3.4 76.5 + + + +
8H G 5.2 3.6 + - - -
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Residues in contact with THR 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C PRO* 5.3 5.4 - - - +
517C GLN* 4.0 10.7 - - + +
518C PRO* 3.2 41.7 - - + +
520C HIS* 1.3 92.0 - - - +
522C LEU* 1.3 62.3 + - - +
524C ASN* 3.7 8.8 + - - +
525C ALA* 2.9 29.8 + - - +
7H T 5.2 3.1 - - - +
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Residues in contact with LEU 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C PRO* 4.3 5.6 - - - +
486C CYS* 3.5 15.7 - - + +
487C LEU* 3.3 54.0 - - + +
490C ARG* 4.4 24.7 - - + +
500C TYR* 3.5 26.2 - - + +
517C GLN* 4.9 6.1 - - + +
518C PRO 3.2 14.4 + - - +
519C LEU* 2.9 12.8 + - + +
521C THR* 1.3 76.5 - - + +
523C ARG* 1.3 72.1 + - + +
525C ALA* 3.1 9.2 + - - +
526C GLU* 2.9 21.1 + - - +
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Residues in contact with ARG 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490C ARG* 4.9 11.6 - - - +
519C LEU* 3.0 22.3 + - + +
520C HIS* 3.8 30.4 + - - +
522C LEU* 1.3 84.7 - - + +
524C ASN* 1.3 63.1 + - - +
526C GLU* 2.9 36.9 + - + +
527C LYS* 3.1 12.1 + - - +
1011C LYS* 5.9 4.5 - - - +
24G C 3.4 31.8 + - - -
25G T 3.3 35.9 + - - +
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Residues in contact with ASN 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 HIS* 2.9 18.9 + - + +
521C THR* 3.7 10.1 + - - +
523C ARG* 1.3 76.5 - - - +
525C ALA* 1.3 62.4 + - - +
527C LYS* 3.2 29.9 + - - +
528C GLU* 4.6 1.2 + - - +
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Residues in contact with ALA 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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483C PRO* 4.0 29.8 - - + +
484C ALA* 5.2 2.2 - - - +
487C LEU* 5.4 2.5 - - + -
521C THR* 2.9 20.0 + - - +
522C LEU* 3.1 6.0 + - - +
524C ASN* 1.3 76.1 - - - +
526C GLU* 1.3 60.4 + - - +
527C LYS 3.7 0.2 + - - -
528C GLU* 4.2 17.8 - - - +
529C LEU* 5.0 4.7 + - - +
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Residues in contact with GLU 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C LEU* 3.5 39.5 - - + -
522C LEU 2.9 9.6 + - - +
523C ARG* 2.9 23.8 + - + +
525C ALA* 1.3 75.2 - - - +
527C LYS* 1.3 73.9 + - - +
528C GLU 2.7 5.0 + - - -
529C LEU* 2.6 32.9 + - - +
530C LEU* 3.1 35.0 + - - +
1011C LYS* 4.2 13.0 + - - +
1015C LEU* 4.2 15.9 - - + +
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Residues in contact with LYS 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 ARG* 3.1 12.1 + - - +
524C ASN* 3.2 26.3 + - - +
526C GLU* 1.3 94.5 + - - +
528C GLU* 1.3 58.2 + - - +
529C LEU 3.4 0.6 + - - -
530C LEU* 4.3 14.9 + - + +
531C PRO 5.6 0.2 - - - +
532C GLY 5.8 0.3 - - - -
533C PHE* 4.0 21.1 - - + +
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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
------------------------------------------------------------
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