Contacts of the helix formed by residues 615 - 627 (chain A) in PDB entry 2A8B
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 ASP 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A SER* 3.2 21.7 + - - -
376A ARG 3.1 30.2 + - - +
377A ILE* 3.8 13.3 + - + +
607A GLN* 3.1 20.9 + - - +
614A VAL* 1.3 71.4 - - - +
616A ALA* 1.3 55.9 + - - +
617A LEU 3.7 1.7 + - - -
618A SER* 3.0 38.7 + - - -
619A ILE* 3.0 33.4 + - + +
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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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376A ARG 4.4 2.0 + - - -
378A LEU* 5.4 3.3 - - + +
614A VAL* 3.6 7.0 + - + +
615A ASP* 1.3 71.4 - - - +
617A LEU* 1.3 65.0 + - - +
619A ILE* 3.6 11.5 - - - +
620A VAL* 3.0 30.2 + - + +
637A TYR* 3.9 4.3 - - + -
640A VAL* 5.3 5.4 - - + -
641A HIS* 3.7 34.1 - - + +
644A LEU* 4.2 20.4 - - + -
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A PRO* 3.8 15.7 - - + +
375A SER 3.8 15.9 - - - +
376A ARG* 3.6 29.9 + - + -
396A GLU* 3.9 17.4 + - + +
399A GLU* 6.3 1.3 - - + -
400A ILE* 3.3 35.7 - - + -
615A ASP* 3.7 6.0 + - - +
616A ALA* 1.3 80.0 - - - +
618A SER* 1.3 63.9 + - - +
620A VAL* 3.2 2.4 + - - +
621A CYS* 3.0 33.6 + - - -
637A TYR* 3.2 17.2 + - - +
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Residues in contact with SER 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A ILE 5.3 3.8 + - - -
0A PRO* 3.5 17.0 - - - -
375A SER* 4.9 0.9 - - - -
615A ASP* 3.0 36.1 + - - -
617A LEU* 1.3 76.3 - - - +
619A ILE* 1.3 59.0 + - - +
621A CYS* 3.2 4.9 + - - +
622A GLN* 2.9 45.0 + - - +
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Residues in contact with ILE 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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600A ALA* 3.8 35.4 - - + +
603A ILE* 4.2 21.1 - - + -
604A GLY* 3.4 34.8 - - - +
607A GLN* 3.8 16.2 - - - +
614A VAL* 4.1 3.6 - - + -
615A ASP 3.0 26.0 + - - +
616A ALA* 3.6 8.5 - - - +
617A LEU 3.3 0.2 - - - -
618A SER* 1.3 77.5 - - - +
620A VAL* 1.3 57.4 - - - +
622A GLN* 3.4 6.5 + - - +
623A LEU* 2.9 32.4 + - + +
644A LEU* 5.9 0.7 - - + -
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ILE* 3.9 18.4 - - + -
600A ALA* 4.4 10.8 - - + -
616A ALA* 3.0 21.9 + - + +
617A LEU 3.7 2.9 - - - +
619A ILE* 1.3 75.8 - - + +
621A CYS* 1.3 58.6 + - - +
623A LEU* 3.3 7.7 + - - +
624A ARG* 3.0 42.9 + - - +
630A MET 3.8 18.4 - - - +
631A VAL* 3.8 23.3 - - + -
637A TYR* 3.7 21.5 - - + -
640A VAL* 5.9 2.7 - - + -
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Residues in contact with CYS 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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0A PRO* 3.5 43.3 - - + -
400A ILE* 3.4 29.8 - - + -
401A PRO* 5.5 1.3 - - - -
617A LEU* 3.0 21.5 + - - -
618A SER* 3.5 9.6 - - - +
620A VAL* 1.3 74.7 - - - +
622A GLN* 1.3 64.2 + - - +
624A ARG* 3.4 5.8 + - - +
625A MET* 3.0 29.7 + - - +
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Residues in contact with GLN 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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-1A ILE* 5.0 11.5 - - - +
0A PRO* 5.6 2.6 - - - +
453A ARG* 3.1 39.8 + - - +
618A SER* 2.9 32.2 + - - +
619A ILE* 3.7 6.5 - - - +
621A CYS* 1.3 77.6 - - - +
623A LEU* 1.3 66.8 + - + +
625A MET* 3.0 27.4 + - - +
626A ASP* 3.1 8.6 + - - +
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Residues in contact with LEU 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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452A ILE* 3.2 32.9 - - + +
453A ARG 4.6 1.6 - - - +
596A GLY 3.7 7.9 - - - +
599A ILE* 3.5 11.9 - - + -
600A ALA* 3.7 39.7 - - + +
603A ILE* 4.0 9.6 - - + -
619A ILE* 2.9 20.5 + - + +
620A VAL* 3.5 12.6 - - - +
622A GLN* 1.3 74.8 - - - +
624A ARG* 1.3 57.2 + - - +
626A ASP* 2.9 10.7 + - - +
627A ARG 2.9 25.3 + - - +
630A MET* 3.8 30.8 - - + +
631A VAL* 4.5 2.2 - - + -
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Residues in contact with ARG 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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397A PHE* 3.1 26.6 + - - -
400A ILE* 2.9 39.1 + - - +
401A PRO 3.1 21.4 + - - +
402A MET* 3.5 30.9 - - - +
403A ASN* 2.5 36.7 + - + +
620A VAL* 3.0 24.3 + - - +
621A CYS* 3.6 6.5 - - - +
623A LEU* 1.3 71.4 - - - +
625A MET* 1.3 56.3 + - - +
626A ASP 3.2 1.5 + - - -
627A ARG 3.5 15.8 + - - -
629A GLY 4.0 1.0 - - - -
630A MET 2.9 31.5 + - - +
631A VAL 2.8 25.3 + - - -
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Residues in contact with MET 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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403A ASN* 3.6 35.9 + - - +
427A ASN* 4.6 5.7 + - - +
430A SER* 4.7 3.8 + - - -
453A ARG* 3.6 15.7 - - - +
621A CYS 3.0 13.9 + - - +
622A GLN* 3.0 23.4 + - - +
624A ARG* 1.3 76.7 - - - +
626A ASP* 1.3 59.8 + - - +
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Residues in contact with ASP 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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427A ASN* 4.1 2.9 - - - +
430A SER* 2.5 31.0 + - - -
450A ASN* 3.3 8.7 + - - +
451A TYR 3.6 6.6 - - - +
452A ILE* 3.5 25.4 - - + +
453A ARG* 2.9 60.8 + - - +
622A GLN* 3.5 12.7 - - - +
623A LEU* 2.9 12.4 + - - +
625A MET* 1.3 80.4 - - - +
627A ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 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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424A ILE* 4.3 7.5 - - - +
425A LEU 5.0 4.5 - - - +
426A PRO* 4.0 3.0 - - - +
427A ASN* 3.4 5.8 - - - +
448A ASN* 2.9 31.7 + - - -
449A ALA 3.6 12.5 - - - +
450A ASN* 2.9 36.6 + - - +
452A ILE* 3.9 7.6 - - + -
464A ALA* 3.5 34.2 + - - -
465A THR* 4.4 0.4 - - - -
466A GLN 4.0 9.1 - - - +
590A ALA 3.0 26.1 + - - -
591A GLY 2.9 18.6 + - - -
592A ILE* 3.5 7.8 - - + +
623A LEU 2.9 4.8 + - - -
624A ARG* 3.5 7.7 - - - -
625A MET 3.6 1.0 - - - -
626A ASP* 1.3 80.7 - - - +
628A GLY* 1.3 76.0 + - - +
629A GLY 3.4 0.9 + - - -
630A MET* 3.0 25.6 + - + +
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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