Contacts of the helix formed by residues 579 - 589 (chain D) in PDB entry 5UHA
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 LEU 579 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731C TYR* 3.4 32.8 - - + -
732C GLU* 3.7 25.4 - - + +
920C HIS* 3.4 19.3 + - + -
924C ARG* 4.1 18.2 - - - +
578D ARG* 1.3 103.4 - - - +
580D ASP* 1.3 73.1 - - - +
581D MET* 3.2 2.2 - - - +
582D VAL* 3.1 17.2 - - - +
583D THR* 3.3 7.4 + - - -
807D ALA* 3.5 5.2 - - - +
808D THR* 3.5 35.2 - - + +
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Residues in contact with ASP 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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725C PRO* 3.6 11.4 - - - +
728C GLY* 5.4 2.3 - - - -
730C ASN* 4.5 2.3 - - - +
731C TYR* 3.9 13.3 - - - +
918C ASN* 2.6 33.2 + - - +
920C HIS* 3.1 33.9 + - + +
579D LEU* 1.3 81.5 - - - +
581D MET* 1.3 56.4 + - - +
583D THR* 3.7 0.3 - - - -
584D GLY* 2.7 29.6 + - - -
720D GLY 4.4 0.2 - - - -
721D PHE* 3.9 15.9 - - + -
724D ALA* 3.2 26.0 - - + +
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Residues in contact with MET 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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731C TYR* 4.4 16.4 - - + +
526D PRO* 4.7 3.6 - - + +
527D LEU* 3.9 22.0 - - + -
577D PRO* 3.6 18.8 - - + -
578D ARG* 3.5 20.2 - - + +
579D LEU 3.2 6.4 - - - +
580D ASP* 1.3 75.6 - - - +
582D VAL* 1.3 60.9 + - - +
584D GLY* 3.1 1.6 + - - -
585D LEU* 2.8 37.0 + - + +
716D LEU 5.2 0.7 - - - +
717D LYS* 3.5 51.8 - - - +
720D GLY* 3.5 8.9 - - - -
721D PHE* 3.5 26.7 - - + -
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Residues in contact with VAL 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D PRO* 4.1 12.4 - - + +
578D ARG* 3.2 29.2 - - - +
579D LEU 3.1 20.6 - - - +
581D MET* 1.3 74.2 - - - +
583D THR* 1.3 51.0 - - - +
585D LEU* 3.8 0.7 - - - +
586D TYR* 2.7 37.9 + - - +
688D MET 4.6 1.6 - - - +
690D LYS* 4.4 11.7 - - + +
693D GLN* 3.9 22.2 + - - +
805D SER* 3.6 25.8 - - - +
806D GLY 4.3 3.1 - - - +
807D ALA* 3.5 16.8 - - + +
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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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725C PRO* 6.0 0.2 - - + -
920C HIS* 3.4 29.9 + - + +
579D LEU 3.3 5.2 + - - -
580D ASP 3.8 3.1 - - - +
581D MET 3.3 0.4 - - - -
582D VAL* 1.3 80.2 - - - +
584D GLY* 1.3 62.7 + - - +
586D TYR* 3.3 8.1 + - - +
587D TYR* 3.0 22.5 + - - +
724D ALA* 4.8 1.8 - - - -
727D SER* 4.1 9.0 - - - +
729D VAL* 3.9 28.3 - - + -
801D THR* 4.7 6.8 + - + +
802D ILE* 4.2 7.6 - - - +
805D SER* 3.9 6.9 + - - -
807D ALA* 3.2 20.9 - - - +
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Residues in contact with GLY 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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580D ASP 2.7 15.6 + - - -
581D MET 3.1 0.4 + - - -
583D THR* 1.3 74.2 - - - +
585D LEU* 1.3 61.3 + - - +
587D TYR* 3.2 18.0 - - - +
588D LEU* 3.7 3.1 + - - +
720D GLY 3.3 23.8 - - - -
723D TRP* 3.5 18.0 - - - +
724D ALA* 3.5 14.6 - - - -
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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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577D PRO* 4.4 13.2 - - + -
581D MET 2.8 21.2 + - - +
584D GLY* 1.3 69.3 - - - -
586D TYR* 1.3 58.5 + - - +
587D TYR 3.0 3.1 + - - -
588D LEU* 3.2 26.3 - - + +
589D THR* 2.6 24.4 + - - +
673D PHE* 4.3 26.7 - - + -
688D MET* 4.4 6.7 - - + -
693D GLN* 3.3 35.9 - - - +
716D LEU* 4.4 13.5 - - + +
719D ALA* 3.8 16.6 - - + -
720D GLY* 3.5 23.1 - - - +
723D TRP* 5.6 0.2 - - + -
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Residues in contact with TYR 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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582D VAL* 2.7 23.1 + - + +
583D THR* 3.7 4.5 - - - +
585D LEU* 1.3 72.6 - - - +
587D TYR* 1.3 54.8 + - - +
589D THR* 3.6 9.6 + - - -
590D THR* 2.5 36.1 + - + -
687D GLN* 3.3 37.0 + - + +
688D MET 3.3 28.1 + - - +
689D HIS* 3.8 13.7 - + + -
801D THR* 4.6 20.2 - - + -
804D ASP* 3.7 14.3 + - + +
805D SER* 3.4 40.6 - - - -
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Residues in contact with TYR 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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1020C PRO* 5.0 2.6 - - - +
1021C TYR* 3.3 29.3 + + - -
583D THR 3.0 12.3 + - - +
584D GLY 3.2 12.1 - - - +
585D LEU 3.0 0.6 - - - -
586D TYR* 1.3 77.0 - - - +
588D LEU* 1.3 76.7 + - + +
590D THR* 2.8 21.2 + - - -
629D VAL* 5.9 2.5 - - + -
630D ARG* 3.2 53.0 + - + +
723D TRP* 4.2 26.0 - + - -
726D ARG 3.5 19.6 + - - -
727D SER* 3.6 37.7 - - - -
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Residues in contact with LEU 588 (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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584D GLY 4.1 7.4 - - - +
585D LEU* 3.2 24.0 - - + +
587D TYR* 1.3 90.7 - - + +
589D THR* 1.3 87.1 + - + +
590D THR 3.1 11.4 + - - +
629D VAL* 3.7 16.0 - - + +
630D ARG* 4.2 7.1 - - - +
667D THR* 3.7 11.8 + - - -
669D GLY* 4.2 29.3 - - - +
672D MET* 5.4 4.7 - - + -
673D PHE* 4.5 9.2 - - + +
719D ALA* 6.4 0.4 - - + -
723D TRP* 3.2 47.1 - - + +
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Residues in contact with THR 589 (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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585D LEU 2.6 21.5 + - - -
586D TYR* 3.6 3.6 + - - -
588D LEU* 1.3 88.6 - - + +
590D THR* 1.3 59.7 + - - +
670D ARG* 2.6 55.2 + - + -
673D PHE* 4.2 11.2 - - + -
686D LYS 3.6 5.6 - - - +
687D GLN* 3.3 6.0 - - - +
688D MET* 3.2 47.3 + - + +
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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