Contacts of the helix formed by residues 617 - 629 (chain A) in PDB entry 5I4A
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 PRO 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A LEU* 3.7 29.2 - - + -
542A VAL* 4.7 6.5 - - + -
568A TYR* 3.4 14.1 - - + +
599A ILE* 3.9 16.6 - - + +
602A LEU* 3.7 28.5 - - + -
603A THR* 3.7 3.3 - - + +
616A LEU* 1.3 89.2 - - + +
618A TYR* 1.3 62.4 + - - +
619A PRO* 3.3 0.9 - - + -
620A LEU* 2.9 24.0 + - + -
621A HIS 2.8 23.9 + - - -
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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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421A ASN* 5.2 3.8 + - - -
463A VAL* 4.1 7.6 - - + -
467A GLY* 3.3 27.3 + - - -
469A ILE* 3.8 15.6 - - + +
602A LEU 3.0 21.0 + - - +
605A VAL* 3.7 16.4 - - + -
606A ALA* 3.6 19.5 - - + +
614A TYR* 3.6 41.0 + + + -
616A LEU 3.4 2.1 + - - -
617A PRO* 1.3 70.9 - - - +
619A PRO* 1.3 69.4 - - + +
621A HIS* 3.1 12.0 + + - +
622A ILE* 2.9 57.8 + - + +
637A ILE* 5.0 3.6 - - + +
638A PRO* 3.9 17.8 - - - +
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Residues in contact with PRO 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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442A TYR* 4.0 15.5 - - + +
443A ILE 3.9 1.3 - - - -
444A GLY* 3.4 23.5 - - - +
461A ALA* 3.5 20.4 - - + +
463A VAL* 3.9 16.8 - - + -
514A LEU* 3.9 23.8 - - + -
602A LEU* 4.2 13.7 - - + -
617A PRO* 3.5 3.1 - - + -
618A TYR* 1.3 94.4 - - + +
620A LEU* 1.3 57.8 + - - +
622A ILE* 3.4 9.1 + - + -
623A ALA* 3.0 24.8 + - - +
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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
----------------------------------------------------------
444A GLY* 3.7 1.1 - - - -
445A ILE 3.5 25.8 - - - +
514A LEU* 3.3 35.7 - - + +
515A ARG 4.2 4.5 - - - +
516A ASP* 3.9 14.1 - - + +
542A VAL* 3.6 44.4 - - + -
616A LEU* 4.5 8.7 - - + -
617A PRO* 2.9 21.7 + - + +
619A PRO* 1.3 75.6 - - - +
621A HIS* 1.3 66.3 + - - +
623A ALA* 3.8 2.8 - - + +
624A ASN* 2.9 33.8 + - - +
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Residues in contact with HIS 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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614A TYR* 3.3 50.0 + + + +
615A LYS 5.5 0.8 + - - -
616A LEU* 4.3 23.1 + - + +
617A PRO 2.8 16.4 + - - +
618A TYR* 3.4 19.3 - + + +
620A LEU* 1.3 73.1 - - - +
622A ILE* 1.3 63.0 + - - +
624A ASN* 3.6 5.0 + - - +
625A LYS* 3.1 52.9 + - + +
636A TYR* 6.0 1.4 - - - +
637A ILE* 4.2 17.0 - - + +
4B A 4.8 5.1 + - - -
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Residues in contact with ILE 622 (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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461A ALA* 3.7 11.7 - - + -
463A VAL* 3.8 15.9 - - + -
469A ILE* 3.7 22.4 - - + -
472A ILE* 3.6 31.0 - - + -
618A TYR* 2.9 53.9 + - + +
619A PRO* 3.7 5.4 - - + +
621A HIS* 1.3 76.8 - - - +
623A ALA* 1.3 58.5 + - - +
625A LYS* 3.1 1.4 + - - +
626A VAL* 2.8 34.0 + - + +
637A ILE* 3.8 23.8 - - + -
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Residues in contact with ALA 623 (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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444A GLY 4.0 15.5 - - - +
445A ILE 4.4 0.7 - - - +
446A ASP* 3.7 21.7 - - + +
459A CYS* 3.6 25.8 - - - +
461A ALA* 4.4 5.2 - - + -
619A PRO 3.0 18.3 + - - +
620A LEU* 3.2 5.4 + - + +
622A ILE* 1.3 77.0 - - - +
624A ASN* 1.3 62.3 + - - +
627A ALA* 3.1 26.9 + - - +
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Residues in contact with ASN 624 (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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446A ASP* 2.6 31.9 - - - +
516A ASP* 3.1 21.6 + - - +
544A LYS* 3.6 19.0 - - - +
616A LEU* 3.4 31.5 - - + +
620A LEU* 2.9 19.8 + - - +
621A HIS* 3.9 4.5 - - - +
623A ALA* 1.3 75.5 - - - +
625A LYS* 1.3 64.4 + - + +
627A ALA* 3.5 2.3 + - - +
628A LEU* 3.2 27.7 + - + +
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Residues in contact with LYS 625 (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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621A HIS* 3.1 47.2 + - + +
622A ILE 3.7 3.6 - - - +
624A ASN* 1.3 77.7 - - + +
626A VAL* 1.3 62.5 + - - +
628A LEU* 3.1 31.3 + - + +
629A THR* 3.8 3.1 + - - -
633A TRP* 3.6 14.1 - - + +
636A TYR* 3.8 37.4 - - + +
637A ILE* 4.4 17.9 - - + -
4B A 4.7 12.7 + - - -
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Residues in contact with VAL 626 (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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459A CYS* 3.7 19.7 - - - -
472A ILE* 3.9 17.9 - - + -
474A LYS* 2.8 37.1 + - + -
622A ILE* 2.8 39.9 + - + +
625A LYS* 1.3 72.3 - - - +
627A ALA* 1.3 58.3 + - - +
629A THR 3.0 9.0 - - - +
633A TRP* 3.6 50.5 - - + +
637A ILE* 4.5 3.4 - - + -
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Residues in contact with ALA 627 (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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446A ASP* 4.0 17.3 - - - +
457A ASN* 6.2 4.7 - - + -
458A LEU 5.5 1.8 - - - -
459A CYS* 3.8 16.7 - - + -
474A LYS* 4.0 16.8 + - + +
476A LYS* 6.1 0.5 - - - -
623A ALA 3.1 20.0 + - - +
624A ASN 3.9 4.0 - - - +
626A VAL* 1.3 76.8 - - - +
628A LEU* 1.3 60.4 + - - +
629A THR 3.4 0.6 + - - -
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Residues in contact with LEU 628 (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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624A ASN* 3.2 15.2 + - + +
625A LYS* 3.1 27.4 + - + +
627A ALA* 1.3 79.4 - - - +
629A THR* 1.3 74.2 + - + +
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Residues in contact with THR 629 (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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384A ASP* 4.4 5.8 - - - +
474A LYS* 2.4 28.9 + - - -
625A LYS 3.8 1.8 + - - +
626A VAL 3.0 6.5 + - - +
627A ALA 3.4 0.2 - - - -
628A LEU* 1.3 97.9 - - + +
630A ASP* 1.3 56.9 + - - +
631A TYR 4.2 0.2 - - - -
632A GLU* 3.8 33.2 - - + +
633A TRP* 3.1 39.2 + - - +
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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