Contacts of the helix formed by residues 607 - 621 (chain A) in PDB entry 5FZ9
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 TRP 607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A VAL* 3.8 21.1 - - + -
472A LEU* 5.9 0.2 - - + -
503A HIS* 3.0 36.2 + - + -
504A TRP* 3.3 22.4 + - - +
505A SER* 3.9 6.2 - - - +
506A TYR* 4.2 13.5 - - + -
583A PRO* 4.3 8.1 - - + -
603A CYS* 3.5 32.1 - - + -
604A THR* 3.1 20.4 + - - +
606A ASP* 1.3 80.9 - - - +
608A LEU* 1.3 84.3 + - + +
609A PRO 3.4 0.4 - - - -
610A LEU* 2.9 22.1 + - + +
611A GLY* 3.0 27.3 + - - +
627A PHE* 4.4 11.2 - + - -
629A HIS* 4.0 16.8 - + - -
632A MET* 3.9 8.7 - - + -
1769A NUK 4.5 5.6 - - - -
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Residues in contact with LEU 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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471A VAL* 4.4 19.5 - - + -
604A THR 3.7 0.2 + - - -
605A VAL* 3.4 9.2 + - + +
607A TRP* 1.3 91.1 - - + +
609A PRO* 1.3 70.7 - - + +
611A GLY 3.2 8.5 + - - -
612A ARG* 3.3 9.9 + - - +
629A HIS* 3.5 15.1 + - + +
632A MET* 3.6 30.7 - - + -
633A ILE* 3.9 15.3 - - + -
636A MET* 4.8 1.8 - - + -
650A THR* 3.9 24.7 - - + +
651A VAL* 3.9 32.8 - - + -
654A ASP* 4.5 9.7 - - + +
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Residues in contact with PRO 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A VAL 4.1 4.7 - - - +
606A ASP 3.5 15.5 - - - +
607A TRP 3.6 0.7 - - - -
608A LEU* 1.3 94.6 - - + +
610A LEU* 1.3 60.3 + - - +
612A ARG* 3.2 5.6 + - + +
613A GLN* 3.1 34.4 + - - +
650A THR* 5.3 4.0 - - + -
654A ASP* 4.7 11.4 - - + +
1769A NUK 4.3 13.0 - - - +
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Residues in contact with LEU 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TRP* 3.7 12.9 - - + -
583A PRO* 3.6 26.2 - - + +
607A TRP* 2.9 15.3 + - + +
609A PRO* 1.3 74.8 - - - +
611A GLY* 1.3 56.6 + - - +
613A GLN* 3.2 24.4 + - - +
614A CYS* 2.7 36.8 + - - +
1764A EDO 3.9 24.2 - - - -
1769A NUK 3.3 63.3 - - + +
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Residues in contact with GLY 611 (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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503A HIS* 4.4 1.9 + - - -
607A TRP* 3.0 42.5 + - - +
608A LEU 3.2 4.4 + - - -
610A LEU* 1.3 77.8 - - - +
612A ARG* 1.3 59.2 + - - +
614A CYS* 3.4 7.1 + - - +
615A VAL* 3.2 28.1 + - - +
629A HIS* 3.7 9.0 + - - -
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Residues in contact with ARG 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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608A LEU 3.3 5.3 + - - +
609A PRO* 3.2 9.9 + - + +
610A LEU 3.2 0.6 - - - -
611A GLY* 1.3 72.4 - - - +
613A GLN* 1.3 66.5 + - + +
615A VAL* 3.3 6.2 + - - +
616A GLU* 3.2 22.9 + - + +
629A HIS* 3.6 20.8 - - - +
630A ASP* 3.1 28.8 + - - -
633A ILE* 4.3 7.1 - - - +
654A ASP* 2.8 56.3 + - - +
657A ILE* 4.0 26.6 - - - +
661A ASP* 4.9 7.0 + - - +
1763A EDO 3.4 19.8 + - - -
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Residues in contact with GLN 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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504A TRP* 4.2 14.2 - - + -
609A PRO* 3.1 26.5 + - - +
610A LEU* 3.6 27.5 - - - +
612A ARG* 1.3 77.0 - - + +
614A CYS* 1.3 57.2 + - - +
616A GLU* 3.4 16.7 + - - +
617A HIS* 3.0 27.5 + - - +
1764A EDO 5.1 3.1 + - - -
1769A NUK 4.9 4.0 + - - -
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Residues in contact with CYS 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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503A HIS* 3.5 19.7 - - - +
504A TRP* 3.4 47.9 - - + -
610A LEU 2.7 20.7 + - - +
611A GLY* 3.6 5.8 - - - +
612A ARG 3.2 0.2 - - - -
613A GLN* 1.3 72.7 - - - +
615A VAL* 1.3 58.9 + - + +
617A HIS* 3.1 2.9 + - - +
618A TYR* 2.8 58.1 + - - -
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Residues in contact with VAL 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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503A HIS* 4.1 24.5 - - + +
611A GLY 3.2 15.0 + - - +
612A ARG* 3.3 7.4 + - - +
614A CYS* 1.3 75.3 - - - +
616A GLU* 1.3 62.1 + - - +
618A TYR* 3.4 10.0 + - + +
619A ARG* 3.1 22.0 + - - +
625A CYS* 4.3 11.7 - - - -
629A HIS* 3.9 26.2 - - + +
697A THR* 4.1 18.9 + - - +
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Residues in contact with GLU 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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612A ARG* 3.2 12.9 + - + +
613A GLN* 3.4 19.3 - - - +
615A VAL* 1.3 78.0 - - - +
617A HIS* 1.3 62.3 + - - +
619A ARG* 3.1 40.4 + - - +
620A LEU* 3.2 31.9 + - + +
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Residues in contact with HIS 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TRP* 4.0 16.0 - + + -
528A GLU* 4.2 9.3 + - - -
531A GLU* 5.1 5.0 + - - -
584A ARG* 3.7 23.0 + - - -
613A GLN 3.0 14.4 + - - +
614A CYS 3.4 8.1 - - - +
616A GLU* 1.3 76.7 - - - +
618A TYR* 1.3 62.8 + - - +
620A LEU* 3.4 15.3 + - + +
621A LEU* 3.1 63.0 + - + +
1760A EPE 3.4 27.5 + - + -
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Residues in contact with TYR 618 (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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501A GLU 4.4 1.7 + - - -
502A ASP* 3.8 5.7 - - - -
503A HIS* 2.9 42.6 + + - -
504A TRP* 4.5 0.9 + - - -
614A CYS* 2.8 38.8 + - - -
615A VAL* 3.6 11.7 - - - +
617A HIS* 1.3 74.6 - - - +
619A ARG* 1.3 57.4 + - - +
621A LEU* 3.3 1.6 + - - +
622A HIS* 2.9 9.0 + - - -
623A ARG* 2.8 87.3 + - + +
624A TYR 3.9 12.3 - - - -
625A CYS* 4.1 18.2 - - - -
1760A EPE 3.7 26.7 + - - -
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Residues in contact with ARG 619 (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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615A VAL* 3.1 12.8 + - - +
616A GLU* 3.1 39.3 + - - +
618A TYR* 1.3 73.5 - - - +
620A LEU* 1.3 83.2 + - + +
622A HIS* 3.0 23.0 + - - -
695A CYS* 3.7 36.9 - - + +
697A THR* 5.0 11.1 + - - +
715A CYS* 4.3 3.1 - - - -
717A HIS* 3.4 53.3 + - - +
718A HIS* 4.3 8.4 - - + -
1770A PO4 4.7 1.0 + - - -
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Residues in contact with LEU 620 (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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616A GLU* 3.2 27.3 + - + +
617A HIS* 3.7 20.0 - - + +
619A ARG* 1.3 95.3 - - + +
621A LEU* 1.3 66.7 + - + +
622A HIS* 3.6 8.9 + - - -
1770A PO4 4.4 9.5 + - - +
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Residues in contact with LEU 621 (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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544A SER* 5.3 4.3 + - - -
617A HIS* 3.1 50.8 + - + +
618A TYR 3.9 4.0 - - - +
619A ARG 3.1 0.4 - - - -
620A LEU* 1.3 85.9 - - + +
622A HIS* 1.3 70.2 + - - +
623A ARG* 3.3 10.1 + - + +
1760A EPE 3.3 43.7 - - - +
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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