Contacts of the helix formed by residues 607 - 617 (chain B) in PDB entry 6UZA
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 PHE 607 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B PHE* 4.7 3.8 - - - -
454B LEU* 3.9 29.2 - - + -
457B LEU* 4.9 6.1 - - + -
458B VAL* 5.0 2.9 - - + -
603B VAL* 3.2 33.9 - - + -
604B VAL 3.4 6.0 + - - +
605B LEU 3.2 1.0 - - - -
606B SER* 1.3 79.2 + - - +
608B SER* 1.3 55.9 + - - +
609B ARG 3.2 4.3 - - - -
610B ILE* 3.3 33.7 - - + +
1003B S9Y 3.5 13.5 - - + +
1005B Y01 3.8 31.0 - - + -
643C MET* 4.6 4.9 - - - -
646C VAL* 4.1 12.1 - - + -
647C ALA* 3.7 35.7 - - + -
650C ILE* 4.3 19.5 - - + -
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Residues in contact with SER 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B TRP* 3.4 33.0 + - - -
529B LEU* 3.4 26.9 - - - +
533B MET* 5.7 0.5 - - - +
604B VAL 4.5 0.6 + - - -
605B LEU* 2.5 24.4 + - - -
606B SER 3.2 0.2 - - - -
607B PHE* 1.3 75.8 - - - +
609B ARG* 1.3 59.5 + - - +
610B ILE 3.2 6.5 + - - -
611B ALA* 3.7 5.7 + - - +
1003B S9Y 4.1 29.4 - - - +
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Residues in contact with ARG 609 (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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450B PHE* 3.7 34.7 - - + +
453B PHE* 6.3 1.1 - - - -
505B MET* 3.5 39.4 + - - +
509B GLU* 4.3 4.8 + - - -
526B TRP* 5.8 0.4 - - - +
530B ASP* 2.6 42.9 + - - +
533B MET* 3.7 22.7 - - + +
534B LEU* 4.9 0.2 - - - +
606B SER* 3.7 3.1 + - - +
607B PHE 3.2 1.6 - - - -
608B SER* 1.3 77.9 - - - +
610B ILE* 1.3 62.1 + - - +
611B ALA 3.1 2.2 - - - -
612B TYR* 3.5 28.5 + - + +
613B ILE* 4.3 2.1 + - - +
762B VAL* 5.6 3.6 - - - +
1002B R0G 3.5 51.2 + - + +
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Residues in contact with ILE 610 (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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450B PHE* 3.7 21.5 - - + -
454B LEU* 4.8 2.7 - - + -
607B PHE* 3.3 36.3 - - + +
608B SER 3.2 0.8 - - - -
609B ARG* 1.3 73.6 - - - +
611B ALA* 1.3 55.9 + - - +
612B TYR 3.1 5.8 + - - -
613B ILE* 3.3 14.2 + - + +
614B LEU* 2.9 45.8 + - + +
1003B S9Y 4.7 6.7 - - + -
1005B Y01 3.7 34.1 - - + -
643C MET* 3.7 36.1 - - + -
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Residues in contact with ALA 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B TRP* 3.7 30.7 - - + +
608B SER 3.7 5.5 + - - +
609B ARG 3.1 0.4 - - - -
610B ILE* 1.3 77.9 - - - +
612B TYR* 1.3 56.0 + - - +
613B ILE 3.5 0.2 - - - -
614B LEU* 4.4 0.7 - - - -
615B PRO* 3.3 18.5 - - - +
624B GLN* 3.3 24.7 + - - +
1003B S9Y 3.4 39.6 - - + +
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Residues in contact with TYR 612 (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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443B PHE* 4.6 2.3 - - - -
526B TRP* 3.5 42.7 + + - +
527B ASN* 3.8 14.0 + - - -
530B ASP* 3.8 17.5 + - - -
609B ARG* 3.5 18.5 + - + +
610B ILE 3.1 1.0 - - - -
611B ALA* 1.3 79.6 - - - +
613B ILE* 1.3 60.3 + - - +
615B PRO* 4.3 0.2 - - - -
749B LEU* 3.3 23.0 - - - +
753B TYR* 4.9 4.5 + - - -
1002B R0G 3.7 68.9 + + + -
1003B S9Y 3.7 26.2 - - - -
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Residues in contact with ILE 613 (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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443B PHE* 3.8 34.3 - - + -
447B ALA* 4.2 13.0 - - + -
450B PHE* 4.5 13.7 - - + -
609B ARG 4.6 1.1 - - - +
610B ILE* 3.6 22.6 - - + +
612B TYR* 1.3 80.3 - - - +
614B LEU* 1.3 64.3 + - - +
615B PRO* 3.6 1.8 - - - -
616B ALA* 3.7 11.0 + - - +
1002B R0G 3.6 33.0 - - + -
1005B Y01 3.9 57.5 - - + +
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Residues in contact with LEU 614 (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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610B ILE* 2.9 25.5 + - + +
613B ILE* 1.3 74.2 - - - +
615B PRO* 1.3 56.0 - - - +
616B ALA 3.1 9.5 + - - -
617B ASN* 3.4 13.7 + - - +
620B PHE* 3.8 35.9 - - + +
621B GLY* 3.8 10.5 + - - -
624B GLN* 3.2 26.9 - - + +
1003B S9Y 5.0 13.9 - - + +
1005B Y01 4.2 17.5 - - + -
640C ILE* 4.8 13.5 - - + -
643C MET* 4.0 28.3 - - + -
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Residues in contact with PRO 615 (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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611B ALA 3.3 16.2 - - - +
612B TYR 4.3 1.3 - - - -
613B ILE 3.8 2.2 - - - -
614B LEU* 1.3 86.9 - - - +
616B ALA* 1.3 58.2 + - - -
617B ASN 3.2 2.2 - - - -
621B GLY* 4.0 16.2 - - - +
624B GLN* 3.3 22.9 - - - +
625B ILE* 6.1 2.7 - - + -
742B TRP* 3.9 9.0 + - + -
745B ALA* 4.9 20.6 - - + +
746B ARG* 3.6 22.2 - - - +
749B LEU* 3.7 22.4 - - + -
1003B S9Y 4.7 8.3 - - - -
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Residues in contact with ALA 616 (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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391B TRP* 5.4 0.4 - - + -
443B PHE* 3.7 30.3 - - + -
613B ILE 3.7 5.1 + - - +
614B LEU 3.1 1.8 - - - -
615B PRO* 1.3 78.7 - - - +
617B ASN* 1.3 57.7 + - - +
746B ARG* 4.2 15.3 + - + -
749B LEU* 3.7 26.0 - - + +
1005B Y01 3.7 34.9 - - + +
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Residues in contact with ASN 617 (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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403B MET* 4.8 17.6 - - - +
613B ILE 4.8 0.2 + - - -
614B LEU 3.4 10.5 + - - +
615B PRO 3.2 1.4 - - - -
616B ALA* 1.3 80.0 - - - +
618B GLU* 1.3 70.6 + - - +
619B SER* 3.3 11.6 + - - +
620B PHE* 3.3 35.6 - - + +
621B GLY* 3.5 9.9 + - - -
742B TRP* 3.3 21.8 + - - -
746B ARG* 5.5 0.9 - - - -
1005B Y01 3.2 37.3 - - + +
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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