Contacts of the helix formed by residues 531 - 539 (chain F) in PDB entry 4CYM
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 THR 531 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501F HIS* 3.5 2.5 - - - -
522F ALA 3.4 14.1 - - - +
523F GLU* 4.2 13.2 - - - +
524F VAL 3.3 10.1 - - - +
525F GLN* 4.5 3.8 - - + -
529F GLY 3.8 0.2 + - - -
530F ASN* 1.3 76.4 - - - +
532F PRO* 1.3 76.1 - - - +
533F LEU* 3.1 11.1 + - - +
534F HIS* 2.8 50.2 + - + +
535F LEU* 3.1 11.4 + - - +
560F ILE* 4.2 22.2 - - + -
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Residues in contact with PRO 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498F THR* 4.2 0.9 - - - +
500F LEU* 3.7 48.7 - - + +
501F HIS* 3.5 35.8 - - + +
504F CYS* 3.4 18.0 - - + +
521F SER 4.6 1.1 - - - +
522F ALA* 3.3 22.0 - - - +
524F VAL 3.8 2.7 - - - +
531F THR* 1.3 82.8 - - - +
533F LEU* 1.3 60.6 + - - +
535F LEU* 3.1 2.6 + - + +
536F ALA* 3.0 20.1 + - - +
548F LEU* 3.9 5.8 - - + -
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Residues in contact with LEU 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F ALA* 4.8 3.3 + - + +
531F THR* 3.0 11.2 + - - +
532F PRO* 1.3 79.9 - - - +
534F HIS* 1.3 63.0 + - - +
535F LEU 3.2 0.2 + - - -
536F ALA* 3.3 1.4 + - - +
537F CYS* 2.9 34.6 + - - -
545F VAL* 4.1 25.1 - - + +
548F LEU* 3.5 29.6 - - + +
549F VAL* 4.7 2.9 - - + -
556F CYS* 4.5 15.3 - - - -
557F ARG 4.6 5.6 - - - +
558F LEU* 4.2 24.5 - - + -
568F PRO* 3.7 27.6 - - + -
584F LEU* 4.6 3.4 - - + -
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Residues in contact with HIS 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F GLY 4.3 4.7 - - - -
530F ASN* 3.3 30.3 - - - +
531F THR* 2.8 52.1 + - + +
533F LEU* 1.3 76.2 - - - +
535F LEU* 1.3 63.2 + - - +
537F CYS* 3.5 4.4 + - - +
538F THR* 3.1 29.2 + - - +
560F ILE* 2.9 35.1 + - + -
562F ASN* 3.7 5.0 + - + -
566F ASP 3.0 20.6 + - - -
568F PRO* 3.8 20.4 - - + +
571F ILE* 3.5 20.5 - - + +
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Residues in contact with LEU 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501F HIS* 3.6 43.5 - - + +
504F CYS 4.4 2.0 - - - -
505F GLN* 4.3 35.4 - - + +
526F ASP* 4.3 7.4 - - - +
530F ASN* 3.9 27.6 - - + +
531F THR 3.1 11.3 + - - +
532F PRO* 3.6 6.3 - - + +
533F LEU 3.1 0.2 - - - -
534F HIS* 1.3 74.8 - - - +
536F ALA* 1.3 66.4 + - - +
538F THR* 2.9 29.3 + - + +
539F TYR* 3.2 13.2 + - + +
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Residues in contact with ALA 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F CYS* 3.6 26.5 + - + +
532F PRO 3.0 15.5 + - - +
533F LEU 3.6 4.7 - - - +
535F LEU* 1.3 75.8 - - - +
537F CYS* 1.3 60.4 + - - +
539F TYR 3.7 0.5 + - - -
540F GLY* 3.2 3.8 + - - -
541F HIS* 3.0 29.6 + - - +
544F CYS* 4.2 6.3 - - + -
545F VAL* 3.9 29.1 - - + +
548F LEU* 4.3 6.1 - - + -
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Residues in contact with CYS 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533F LEU* 2.9 33.1 + - - +
534F HIS 3.8 4.9 - - - +
535F LEU 3.1 0.2 - - - -
536F ALA* 1.3 75.7 - - - +
538F THR* 1.3 63.6 - - - +
539F TYR 3.3 0.3 + - - -
540F GLY* 3.3 2.7 + - - -
545F VAL* 4.0 6.1 - - - -
568F PRO* 3.7 39.5 - - + +
571F ILE* 3.7 10.0 - - + +
572F ALA* 4.5 3.7 - - - +
577F TYR* 3.3 23.4 - - - -
580F VAL* 3.9 24.6 - - + +
584F LEU* 4.1 4.5 - - - -
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Residues in contact with THR 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530F ASN* 5.7 4.0 - - - +
534F HIS* 3.1 16.9 + - + +
535F LEU* 2.9 24.3 + - + +
537F CYS* 1.3 76.0 - - - +
539F TYR* 1.3 84.5 + - - +
540F GLY 3.5 0.2 - - - -
571F ILE* 3.3 30.7 - - + -
575F TRP* 3.5 23.3 - - - +
577F TYR* 3.3 14.7 + - - -
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Residues in contact with TYR 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505F GLN* 3.2 56.6 + - + -
535F LEU* 3.2 10.8 + - + +
536F ALA 3.7 0.2 + - - -
538F THR* 1.3 102.9 + - - +
540F GLY* 1.3 63.0 + - - +
541F HIS* 3.1 29.9 + + + +
575F TRP* 5.0 15.0 - + - -
577F TYR* 3.7 9.7 + - - -
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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