Contacts of the helix formed by residues 534 - 541 (chain D) in PDB entry 1C2O
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 534 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A TRP* 3.8 43.9 - - + +
388A PRO* 6.3 1.0 - - - +
526D ALA 5.6 0.2 + - - -
529D CYS 5.3 0.4 + - - -
530D ALA* 2.7 34.1 + - + +
533D ASN* 1.3 79.1 - - + +
535D PHE* 1.3 61.3 + - + +
536D LEU 3.8 0.2 - - - -
537D PRO* 3.8 5.9 - - - +
538D LYS* 3.0 25.9 + - - +
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Residues in contact with PHE 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU* 4.0 24.2 - - + -
376A GLU* 4.5 14.6 - - + -
377A ALA* 4.3 29.6 - - + -
380A LEU* 3.8 37.2 - - + -
535A PHE* 5.2 7.2 - + - -
539A LEU* 4.9 6.5 - - + -
377D ALA* 4.7 4.3 - - + -
530D ALA 3.3 1.7 + - - +
531D PHE* 3.2 23.3 + + - +
534D ARG* 1.3 76.6 - - + +
536D LEU* 1.4 69.9 + - - +
537D PRO* 3.2 2.7 - - - -
538D LYS* 2.8 30.6 + - + +
539D LEU* 3.0 38.2 + - + -
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Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D VAL* 5.1 4.9 - - + -
374D ALA* 3.8 28.0 - - + +
377D ALA* 4.4 0.2 - - + -
378D VAL* 4.5 5.4 - - + -
405D HIS* 5.4 2.7 - - + -
531D PHE* 2.7 42.1 + - + +
532D TRP* 3.5 38.6 - - + +
535D PHE* 1.4 73.0 - - - +
537D PRO* 1.3 62.1 - - + +
539D LEU* 2.9 21.4 + - + +
540D LEU* 2.8 49.0 + - + +
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Residues in contact with PRO 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D TRP 2.9 26.0 - - - +
533D ASN* 3.8 12.8 - - - +
534D ARG 3.8 8.5 - - - +
535D PHE 3.3 4.3 - - - -
536D LEU* 1.3 88.0 - - + +
538D LYS* 1.3 59.1 + - + +
540D LEU* 2.8 12.8 + - + +
541D SER* 2.8 31.4 + - - -
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Residues in contact with LYS 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU* 4.8 10.8 - - + +
376A GLU* 4.4 27.8 + - + +
534D ARG 3.0 22.8 + - - +
535D PHE* 2.8 32.1 + - + +
537D PRO* 1.3 76.1 - - + +
539D LEU* 1.3 60.5 + - - +
541D SER* 3.2 12.1 + - - +
542D ALA* 3.2 23.0 + - - +
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Residues in contact with LEU 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A LEU* 4.2 22.1 - - + +
535A PHE* 4.9 4.3 - - + -
539A LEU* 4.7 5.4 - - + -
373D LEU* 4.1 29.8 - - + +
374D ALA* 3.7 19.1 - - + +
377D ALA* 3.7 30.5 - - + -
535D PHE* 3.0 29.0 + - + +
536D LEU* 2.9 18.9 + - + +
538D LYS* 1.3 77.6 - - - +
540D LEU* 1.3 63.9 + - - +
542D ALA* 3.1 5.7 + - - +
543D THR* 2.8 33.5 + - + +
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Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D VAL* 5.8 0.2 - - + -
369D GLN* 4.0 28.7 - - + +
370D ALA* 3.8 7.2 - - + -
371D SER* 3.6 18.8 - - - +
374D ALA* 3.2 29.6 - - + -
536D LEU* 2.8 35.8 + - + +
537D PRO* 2.8 11.4 + - + +
539D LEU* 1.3 79.6 - - - +
541D SER* 1.3 56.1 + - - +
542D ALA 3.1 2.4 + - - -
543D THR* 3.1 30.0 + - - +
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Residues in contact with SER 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D PRO 2.8 22.3 + - - -
538D LYS* 3.2 14.8 + - - +
540D LEU* 1.3 70.7 - - - +
542D ALA* 1.3 58.2 + - - +
543D THR 5.0 0.4 - - - -
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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