Contacts of the helix formed by residues 607 - 617 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 4.7 4.3 - - - -
454A LEU* 3.9 28.5 - - + -
457A LEU* 4.9 5.6 - - + -
458A VAL* 5.0 2.7 - - + -
603A VAL* 3.2 34.1 - - + -
604A VAL 3.4 5.7 + - - +
605A LEU 3.2 1.0 - - - -
606A SER* 1.3 79.1 + - - +
608A SER* 1.3 54.6 + - - +
609A ARG 3.2 4.7 - - - -
610A ILE* 3.3 34.1 - - + +
1002A S9Y 3.5 14.2 - - + +
1004A Y01 3.8 30.7 - - + -
643B MET* 4.6 5.4 - - - -
646B VAL* 4.1 12.8 - - + -
647B ALA* 3.7 35.7 - - + -
650B ILE* 4.3 20.4 - - + -
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Residues in contact with SER 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A TRP* 3.4 32.2 + - - -
529A LEU* 3.4 27.5 - - - +
533A MET* 5.7 0.3 - - - +
604A VAL 4.5 0.6 + - - -
605A LEU* 2.5 24.4 + - - -
606A SER 3.2 0.2 - - - -
607A PHE* 1.3 75.2 - - - +
609A ARG* 1.3 59.2 + - - +
610A ILE 3.2 6.1 + - - -
611A ALA* 3.7 6.1 + - - +
1002A S9Y 4.1 29.8 - - - +
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Residues in contact with ARG 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 3.7 33.4 - - + -
453A PHE* 6.3 1.1 - - - -
505A MET* 3.5 38.9 + - - +
509A GLU* 4.3 5.3 + - - -
526A TRP* 5.8 0.7 - - - +
530A ASP* 2.6 44.0 + - - +
533A MET* 3.7 24.0 - - + +
606A SER 3.7 2.6 + - - +
607A PHE 3.2 1.8 - - - -
608A SER* 1.3 77.8 + - - +
610A ILE* 1.3 63.0 + - - +
611A ALA 3.1 2.0 - - - -
612A TYR* 3.5 27.8 + - + +
613A ILE* 4.3 2.3 + - - +
762A VAL* 5.6 4.2 - - - +
1001A R0G 3.5 50.0 + - + +
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Residues in contact with ILE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A PHE* 3.7 20.6 - - + -
454A LEU* 4.8 3.6 - - + -
607A PHE* 3.3 34.5 - - + +
608A SER 3.2 0.8 - - - -
609A ARG* 1.3 74.9 - - - +
611A ALA* 1.3 55.3 + - - +
612A TYR 3.1 5.2 - - - -
613A ILE* 3.3 14.2 + - + -
614A LEU* 2.9 46.1 + - + +
1002A S9Y 4.7 6.7 - - + -
1004A Y01 3.7 33.2 - - + -
643B MET* 3.7 36.6 - - + -
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A TRP* 3.7 30.3 - - + +
608A SER 3.7 5.9 + - - +
609A ARG 3.1 0.8 - - - -
610A ILE* 1.3 77.5 - - - +
612A TYR* 1.3 55.8 + - - +
613A ILE 3.5 0.4 - - - -
614A LEU* 4.4 0.2 - - - -
615A PRO* 3.3 19.3 - - - +
624A GLN* 3.3 25.4 + - - +
1002A S9Y 3.4 40.0 - - + +
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Residues in contact with TYR 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 4.6 2.3 - - - -
526A TRP* 3.5 44.4 + + - +
527A ASN* 3.8 14.6 + - - -
530A ASP* 3.8 17.7 + - - -
609A ARG* 3.5 19.2 + - + +
610A ILE 3.1 1.2 - - - -
611A ALA* 1.3 78.7 - - - +
613A ILE* 1.3 60.6 + - - +
615A PRO* 4.3 0.2 - - - -
749A LEU* 3.3 23.6 - - - +
753A TYR* 4.9 4.3 + - - -
1001A R0G 3.7 67.3 + - + +
1002A S9Y 3.7 26.7 - - - -
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Residues in contact with ILE 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A PHE* 3.8 32.9 - - + -
447A ALA* 4.2 14.4 - - + -
450A PHE* 4.5 14.4 - - + -
609A ARG 4.6 1.1 - - - +
610A ILE* 3.6 22.4 - - + +
612A TYR* 1.3 81.5 - - - +
614A LEU* 1.3 66.0 + - - +
615A PRO* 3.6 1.6 - - - -
616A ALA* 3.7 10.7 + - - +
749A LEU* 4.9 0.4 - - - -
1001A R0G 3.6 32.3 - - + -
1004A Y01 3.9 57.1 - - + +
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Residues in contact with LEU 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A ILE* 2.9 27.0 + - + +
613A ILE* 1.3 73.6 - - - +
615A PRO* 1.3 56.8 - - + +
616A ALA 3.1 10.1 + - - -
617A ASN* 3.4 14.2 + - - +
620A PHE* 3.8 35.0 - - + +
621A GLY* 3.8 10.2 + - - -
624A GLN* 3.2 26.7 - - + +
1002A S9Y 5.0 13.5 - - + +
1004A Y01 4.2 17.5 - - + -
640B ILE* 4.8 13.0 - - + -
643B MET* 4.0 29.2 - - + -
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Residues in contact with PRO 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A ALA 3.3 16.4 - - - +
612A TYR 4.3 0.9 - - - -
613A ILE 3.8 2.7 - - - -
614A LEU* 1.3 84.8 - - - +
616A ALA* 1.3 57.8 + - - -
617A ASN 3.2 2.4 + - - -
621A GLY* 4.0 15.9 - - - +
624A GLN* 3.3 23.1 - - - +
625A ILE* 6.1 2.5 - - + -
742A TRP* 3.9 8.7 + - + -
745A ALA* 4.9 21.3 - - + +
746A ARG* 3.6 22.9 - - - +
749A LEU* 3.7 22.0 - - + -
1002A S9Y 4.7 8.5 - - - -
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Residues in contact with ALA 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TRP* 5.4 0.4 - - + -
443A PHE* 3.7 30.1 - - + -
613A ILE 3.7 4.9 + - - +
614A LEU 3.1 2.0 - - - -
615A PRO* 1.3 78.2 - - - +
617A ASN* 1.3 59.4 + - - +
618A GLU 4.3 0.2 + - - -
746A ARG* 4.2 14.8 + - + -
749A LEU* 3.7 26.4 - - + +
750A TRP* 5.3 0.2 - - - +
1004A Y01 3.7 36.2 - - + +
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Residues in contact with ASN 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A MET* 4.8 18.2 - - - +
613A ILE 4.8 0.2 + - - -
614A LEU 3.4 11.3 + - - +
615A PRO 3.2 0.6 - - - -
616A ALA* 1.3 80.4 - - - +
618A GLU* 1.3 70.1 + - - +
619A SER* 3.3 11.7 + - - +
620A PHE* 3.3 35.2 - - + +
621A GLY* 3.5 10.1 + - - -
742A TRP* 3.3 21.2 + - - -
746A ARG* 5.5 0.4 - - - -
1004A Y01 3.2 37.5 - - + +
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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