Contacts of the helix formed by residues 577 - 587 (chain D) 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 TYR 577 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D CYS 3.4 26.2 - - - -
538D THR 3.3 9.0 + - - -
539D TYR* 3.7 5.2 + - - -
540D GLY* 3.4 27.3 + - - -
572D ALA* 3.0 17.7 + - + +
575D TRP* 3.2 58.8 - + + -
576D GLY* 1.3 72.4 - - - -
578D GLN* 1.3 65.4 + - - +
579D GLY 3.0 4.1 + - - -
580D VAL* 3.2 18.6 + - + -
581D ILE* 3.0 22.7 + - - +
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Residues in contact with GLN 578 (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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576D GLY 3.7 4.9 + - - -
577D TYR* 1.3 73.4 - - - +
579D GLY* 1.3 58.7 + - - +
581D ILE* 3.1 13.0 + - - +
582D GLU* 2.8 55.8 + - + +
609D LYS* 6.2 0.3 - - - +
610D ILE* 5.6 8.0 - - + +
613D VAL* 3.3 33.4 - - + +
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Residues in contact with GLY 579 (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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542D GLU* 3.6 25.6 - - - +
577D TYR 3.0 1.4 + - - -
578D GLN* 1.3 79.4 - - - +
580D VAL* 1.3 57.9 + - - +
582D GLU* 3.3 10.8 + - - +
583D THR* 2.7 34.4 + - - -
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Residues in contact with VAL 580 (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 CYS* 3.9 15.7 - - + -
540D GLY* 4.3 11.2 - - - -
542D GLU* 3.7 32.5 - - + +
545D VAL* 4.1 13.7 - - + -
572D ALA* 3.5 23.1 - - + -
577D TYR* 3.3 24.0 - - + +
579D GLY* 1.3 72.3 - - - +
581D ILE* 1.3 65.3 + - - +
583D THR* 3.0 10.7 + - - -
584D LEU* 2.9 35.2 + - + +
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Residues in contact with ILE 581 (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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569D LEU* 4.0 16.3 - - + +
572D ALA* 3.5 36.3 - - + +
573D ALA* 4.2 2.9 - - - +
576D GLY 4.3 0.9 - - - -
577D TYR 3.0 28.3 + - - +
578D GLN* 3.1 11.9 + - + +
580D VAL* 1.3 81.7 - - - +
582D GLU* 1.3 63.9 + - - +
584D LEU* 3.2 3.0 + - - +
585D LEU* 3.0 42.2 + - + +
610D ILE* 4.1 24.9 - - + -
613D VAL* 5.1 7.4 - - + -
614D MET* 4.0 15.9 - - + -
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Residues in contact with GLU 582 (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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578D GLN* 2.8 48.4 + - - +
579D GLY* 3.7 8.0 - - - +
581D ILE* 1.3 73.1 - - - +
583D THR* 1.3 53.8 + - - +
585D LEU* 3.1 7.1 + - - +
586D GLN* 2.7 53.0 + - - +
613D VAL* 4.0 19.1 - - + +
617D TYR* 3.9 16.3 + - - +
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Residues in contact with THR 583 (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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542D GLU* 4.2 2.3 + - - +
545D VAL* 4.4 13.0 - - + -
546D LYS* 3.7 42.5 - - + -
549D VAL* 4.8 6.0 - - + +
550D TYR* 4.2 17.7 - - + +
579D GLY 2.7 23.2 + - - -
580D VAL* 3.2 10.3 - - - -
582D GLU* 1.3 75.9 - - - +
584D LEU* 1.3 64.0 + - - +
586D GLN* 3.4 11.8 + - - +
587D ASN* 3.0 29.9 + - - +
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Residues in contact with LEU 584 (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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533D LEU* 4.6 3.6 - - + -
537D CYS* 4.1 3.4 - - - -
545D VAL* 4.5 8.5 - - + -
549D VAL* 4.4 13.9 - - + -
558D LEU* 3.8 28.3 - - + +
568D PRO* 4.0 17.0 - - + +
569D LEU* 3.8 38.4 - - + +
572D ALA* 4.2 1.3 - - + -
580D VAL* 2.9 38.4 + - + +
581D ILE 3.5 6.3 - - - +
583D THR* 1.3 71.5 - - - +
585D LEU* 1.3 64.7 + - - +
587D ASN* 3.1 6.4 + - - -
588D GLY 3.0 16.3 + - - -
589D ALA* 3.1 20.5 + - + +
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Residues in contact with LEU 585 (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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569D LEU* 3.9 26.2 - - + -
581D ILE* 3.0 43.7 + - + +
582D GLU* 3.6 3.4 - - - +
584D LEU* 1.3 77.1 - - - +
586D GLN* 1.3 59.4 + - - +
588D GLY* 2.9 20.1 + - - -
589D ALA* 4.0 14.7 - - - +
591D THR* 4.3 16.2 - - + +
613D VAL* 4.5 2.0 - - + +
614D MET* 4.3 14.1 - - + +
617D TYR* 3.9 50.8 - - + -
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Residues in contact with GLN 586 (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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47A HIS* 4.5 21.4 + - - -
63A ALA* 6.0 2.0 - - - +
64A LEU* 3.5 28.2 + - + +
550D TYR* 4.7 10.5 + - - +
582D GLU* 2.7 39.8 + - - +
583D THR* 3.7 12.4 - - - +
584D LEU 3.2 0.2 - - - -
585D LEU* 1.3 75.9 - - - +
587D ASN* 1.3 62.4 + - - +
588D GLY 3.4 0.2 - - - -
617D TYR* 3.5 25.8 + - + +
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Residues in contact with ASN 587 (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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64A LEU* 3.9 21.6 - - - +
78A GLN* 5.5 2.0 + - - -
549D VAL* 3.6 29.3 + - + +
550D TYR* 3.3 35.5 + - - -
558D LEU* 3.6 14.7 - - + +
583D THR 3.0 20.8 + - - +
584D LEU 3.1 6.0 + - - +
585D LEU 3.1 0.4 - - - -
586D GLN* 1.3 81.8 - - - +
588D GLY* 1.3 56.6 + - - +
589D ALA 3.7 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