Contacts of the helix formed by residues 522 - 534 (chain C) in PDB entry 5U07
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 ARG 522 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C TYR* 4.1 16.2 - - - +
521C GLU* 1.3 88.2 - - + +
523C PRO* 1.3 76.9 - - + +
524C ARG* 3.1 5.2 + - + +
525C VAL* 3.4 40.2 - - + +
526C ALA* 3.0 18.4 + - - +
198D THR* 4.4 14.1 + - - -
199D VAL 4.7 8.7 + - - -
200D GLU* 2.7 33.7 + - - -
201D VAL* 5.4 8.3 - - - +
29H VAL* 5.3 5.1 - - - +
166J ARG* 6.1 0.2 - - + -
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Residues in contact with PRO 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521C GLU 3.4 4.4 - - - +
522C ARG* 1.3 88.3 - - + +
524C ARG* 1.3 56.6 + - + +
526C ALA* 3.3 8.4 + - + +
527C LYS 2.9 18.9 + - - -
162J HIS* 2.8 65.3 - - + +
165J ALA* 3.8 22.4 - - + +
166J ARG* 4.1 20.4 - - + +
214J VAL* 4.0 11.7 - - + +
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Residues in contact with ARG 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLU 4.3 3.8 + - - -
444C SER* 3.2 27.5 + - - +
445C ASN* 4.5 1.0 - - - +
446C SER* 3.3 10.7 - - - +
522C ARG* 3.2 4.4 - - + +
523C PRO* 1.3 77.5 - - - +
525C VAL* 1.3 65.0 + - + +
527C LYS* 2.7 26.3 + - + +
528C VAL* 3.1 12.6 + - + +
20H ASP* 3.7 9.7 + - - -
21H ASP* 2.7 41.4 + - - -
22H LEU* 3.2 34.7 - - + +
162J HIS* 3.4 12.4 + - + +
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Residues in contact with VAL 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C TRP* 6.3 0.2 - - + -
444C SER* 3.8 29.4 - - - +
445C ASN 5.4 0.2 - - - +
465C TRP* 4.2 8.3 - - + -
519C TYR* 3.0 26.7 - - + +
522C ARG* 3.3 36.9 + - + +
524C ARG* 1.3 80.2 - - + +
526C ALA* 1.3 58.3 + - - +
528C VAL* 3.1 7.5 - - - +
529C VAL* 2.9 44.8 + - + +
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Residues in contact with ALA 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C CYS* 3.1 45.2 - - - +
521C GLU 4.8 0.2 - - - +
522C ARG 3.0 10.7 + - - +
523C PRO* 3.5 9.9 - - + +
525C VAL* 1.3 76.8 - - - +
527C LYS* 1.3 62.5 + - - +
530C GLU* 3.0 29.8 + - - +
214J VAL* 3.9 19.3 - - + -
215J GLN* 4.9 2.2 - - + +
218J HIS* 4.0 2.3 + - - -
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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 PRO 2.9 10.6 + - - +
524C ARG* 2.7 19.0 + - + +
526C ALA* 1.3 72.3 - - - +
528C VAL* 1.3 64.2 + - - +
531C ARG* 3.0 52.4 + - + +
155J ASP* 6.0 2.2 - - - -
158J GLU* 3.4 30.5 - - + +
162J HIS* 3.7 9.6 - - + +
218J HIS* 3.1 29.8 + - + -
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Residues in contact with VAL 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ALA* 3.6 15.5 - - - +
443C GLU* 3.5 21.8 - - + +
444C SER* 3.4 32.8 - - - +
524C ARG* 3.1 3.7 + - + +
525C VAL* 3.1 17.0 - - - +
527C LYS* 1.3 81.9 - - - +
529C VAL* 1.3 73.4 + - + +
531C ARG* 3.1 11.3 + - - +
532C HIS* 2.9 52.7 + - + -
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Residues in contact with VAL 529 (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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440C ALA* 4.5 5.6 - - + -
465C TRP* 3.3 38.8 - - + -
512C TYR* 2.7 36.1 + - + +
516C THR* 3.3 26.7 - - + +
519C TYR 4.7 2.0 - - - +
520C CYS* 4.1 14.8 - - - -
525C VAL* 2.9 31.6 + - + +
526C ALA 4.0 1.8 - - - +
528C VAL* 1.3 75.6 - - + +
530C GLU* 1.3 62.1 + - + +
532C HIS* 3.4 0.5 + - - -
533C ARG* 2.9 17.0 + - - +
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Residues in contact with GLU 530 (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 CYS* 3.8 10.2 - - - -
526C ALA 3.0 16.5 + - - +
529C VAL* 1.3 76.2 - - + +
531C ARG* 1.3 62.2 + - - +
532C HIS 3.0 2.0 - - - -
533C ARG* 2.7 28.5 + - + +
534C SER* 3.0 13.2 + - - -
215J GLN* 2.9 47.8 - - - +
218J HIS* 3.7 15.6 - - + +
219J ARG* 2.3 54.0 + - + +
222J GLU* 4.7 3.5 - - - +
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Residues in contact with ARG 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLU* 3.5 23.3 + - - +
527C LYS* 3.0 43.4 + - + +
528C VAL* 3.9 9.6 + - - +
530C GLU* 1.3 76.0 - - - +
532C HIS* 1.3 76.7 + - - +
534C SER* 2.8 19.8 + - - -
535C THR* 4.4 4.7 - - - +
218J HIS* 5.3 3.7 - - + +
222J GLU* 4.1 20.4 - - + +
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Residues in contact with HIS 532 (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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435C LYS* 5.9 4.2 + - - +
436C ALA* 3.9 21.1 + - + +
439C GLU* 3.9 19.9 + - - +
440C ALA* 3.7 25.1 - - + -
443C GLU* 2.4 37.3 + - - -
512C TYR* 4.6 2.7 - - - +
528C VAL* 2.9 39.0 + - + +
529C VAL 3.7 2.7 - - - +
531C ARG* 1.3 92.7 + - - +
533C ARG* 1.3 61.4 + - - +
534C SER 3.3 1.6 - - - -
535C THR* 3.0 30.9 + - + +
536C LEU* 4.1 0.7 - - - +
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Residues in contact with ARG 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C LEU* 3.9 28.6 - - + +
512C TYR* 3.4 24.8 - - + -
513C ASP* 2.9 44.8 + - - -
529C VAL 2.9 15.9 + - - +
530C GLU* 2.7 19.5 + - - +
532C HIS* 1.3 73.6 - - - +
534C SER* 1.3 65.5 + - - +
535C THR 3.0 3.9 + - - -
536C LEU* 3.0 21.2 + - - +
537C PHE* 3.2 33.8 + - - -
219J ARG* 4.0 33.5 - - - +
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Residues in contact with SER 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C GLU 3.0 6.5 + - - -
531C ARG 2.8 23.0 + - - -
533C ARG* 1.3 77.6 - - - +
535C THR* 1.3 65.2 + - - +
537C PHE* 3.2 35.5 + - - +
538C SER 4.6 0.5 + - - -
222J GLU* 3.2 46.0 + - - -
226J ARG* 4.0 9.6 - - - -
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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