Contacts of the helix formed by residues 689 - 698 (chain B) in PDB entry 5UO5
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 SER 689 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A ASP* 2.4 40.6 + - - +
635A LEU* 4.5 5.7 - - - +
687A PRO 3.7 5.2 - - - -
688A MET* 4.2 8.0 - - - +
689A SER 3.5 11.7 - - - +
656B HIS* 4.1 6.7 - - - -
688B MET* 1.3 81.4 - - - +
690B GLY* 1.3 65.5 + - - +
691B SER 3.4 2.5 - - - -
692B ILE* 3.1 33.1 + - - +
693B THR* 3.7 6.8 + - - +
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Residues in contact with GLY 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PRO 5.9 0.2 - - - -
687A PRO* 3.1 11.7 + - - -
688A MET* 4.3 0.4 - - - +
689A SER 5.0 0.2 - - - +
690A GLY 5.8 0.4 - - - +
685B VAL* 3.9 22.1 - - - +
686B PRO* 4.3 4.7 + - - -
688B MET 3.1 6.8 + - - -
689B SER* 1.3 74.8 - - - +
691B SER* 1.3 60.0 + - - +
693B THR* 2.7 25.9 + - - -
696B PHE* 3.2 17.1 - - - +
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Residues in contact with SER 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A VAL* 3.0 32.4 - - - +
601A ARG* 3.6 10.9 - - - -
604A CYS 5.7 0.2 - - - +
605A ASP* 4.4 6.6 + - - +
687A PRO* 3.0 22.4 + - - +
312B GLU* 4.8 1.9 - - - +
690B GLY* 1.3 72.5 - - - +
692B ILE* 1.3 59.7 + - - +
693B THR 3.2 2.3 + - - -
696B PHE* 3.4 32.2 - - - -
697B HIS* 2.9 25.8 + - - -
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Residues in contact with ILE 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A VAL* 4.7 0.7 - - + -
604A CYS* 4.4 15.7 - - + +
605A ASP* 6.1 0.2 - - - +
606A ASN* 6.4 0.4 - - - -
612A LEU* 4.2 19.7 - - + -
631A LYS* 3.9 49.5 + - + +
632A ASP 4.1 0.4 - - - +
635A LEU* 4.1 28.3 - - + -
687A PRO 4.8 0.2 + - - -
312B GLU* 6.2 0.2 - - - -
657B HIS* 4.0 18.0 + - + -
689B SER* 3.1 36.8 + - - +
691B SER* 1.3 83.6 - - - +
693B THR* 1.3 60.8 + - - +
694B PRO* 4.7 1.0 - - - +
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Residues in contact with THR 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLU* 5.6 0.9 - - - -
656B HIS* 4.1 19.5 - - + +
657B HIS* 3.8 20.6 - - - +
660B THR* 3.4 22.0 - - - +
686B PRO* 3.6 11.7 - - + +
689B SER 3.9 10.8 - - - +
690B GLY 2.7 20.7 + - - +
691B SER 3.8 4.7 - - - +
692B ILE* 1.3 80.8 - - - +
694B PRO* 1.3 69.9 - - - +
695B VAL* 3.3 16.5 + - - +
696B PHE* 3.4 11.8 + - - +
697B HIS* 3.9 3.4 - - - -
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Residues in contact with PRO 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ASN* 3.8 14.9 + - - +
312B GLU* 4.3 18.6 - - - +
657B HIS* 4.9 3.6 - - - +
660B THR* 3.5 8.3 - - - +
661B GLU* 3.9 23.6 - - + +
664B ILE* 3.8 25.6 - - + -
692B ILE 4.7 1.1 - - - +
693B THR* 1.3 88.0 - - + +
695B VAL* 1.3 63.2 + - - +
696B PHE 3.2 0.6 + - - -
697B HIS* 3.4 12.1 + - + +
698B GLN* 3.7 6.4 + - - +
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Residues in contact with VAL 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660B THR* 3.6 42.4 - - + +
663B PHE* 3.9 13.2 - - + -
664B ILE* 4.0 8.3 - - + -
681B TRP* 3.2 12.0 + - - -
684B ILE* 3.8 18.6 - - + +
685B VAL* 3.9 12.6 - - + -
686B PRO* 3.9 10.8 - - + -
693B THR* 3.5 16.6 - - - +
694B PRO* 1.3 75.5 - - - +
696B PHE* 1.3 67.6 + - - +
698B GLN* 3.1 20.7 + - - +
700B MET* 3.5 14.0 - - + +
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Residues in contact with PHE 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A ARG* 3.8 22.7 - - - -
682A VAL 5.1 1.1 - - - -
685A VAL 5.4 3.6 - - - -
686A PRO 5.3 1.1 - - - -
687A PRO* 4.2 19.3 - - + -
802A H4B 2.8 60.9 + + - +
681B TRP* 3.1 45.5 + + - -
685B VAL* 4.1 6.1 - - + -
690B GLY* 3.2 23.8 - - - +
691B SER* 3.4 38.6 - - - -
693B THR 3.4 5.3 + - - +
694B PRO 3.2 0.2 - - - -
695B VAL* 1.3 81.4 - - - +
697B HIS* 1.3 64.5 + + + +
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Residues in contact with HIS 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A ARG* 3.5 28.5 + - - -
605A ASP* 3.7 18.8 + - - -
802A H4B 3.4 12.2 + - - +
310B ASN* 3.4 5.0 - - - +
311B TRP* 2.9 37.1 + - + +
312B GLU* 3.5 50.5 + - + +
691B SER 2.9 26.1 + - - -
693B THR 3.9 11.0 - - - -
694B PRO 3.4 6.2 + - - +
695B VAL 3.2 0.6 - - - -
696B PHE* 1.3 87.6 - + + +
698B GLN* 1.3 59.0 + - - +
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Residues in contact with GLN 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A H4B 3.5 2.7 - - - -
308B VAL* 4.6 7.7 - - - +
309B LYS 4.0 12.5 + - - -
310B ASN* 2.7 29.4 + - - +
315B VAL 5.4 0.6 + - - -
317B LEU* 4.7 9.0 - - - +
664B ILE* 3.7 18.4 - - + +
667B MET* 3.7 35.4 - - - +
681B TRP* 3.3 23.4 - - - -
694B PRO 3.7 10.5 + - - +
695B VAL* 3.1 12.8 + - - +
696B PHE 3.2 0.6 - - - -
697B HIS* 1.3 77.0 - - - +
699B GLU* 1.3 87.8 + - - +
700B MET* 3.4 6.7 + - + +
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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