Contacts of the helix formed by residues 616 - 625 (chain A) in PDB entry 3DKO
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 616 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A TYR* 3.6 14.3 - - - +
615A GLU* 1.3 81.8 + - - +
617A PRO* 1.4 71.0 - - + +
618A ASN* 4.6 10.5 - - + +
619A ARG* 3.2 31.8 + - - +
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Residues in contact with PRO 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A PRO* 4.7 12.7 - - + +
612A GLU* 6.4 2.0 - - + -
614A TYR 4.5 2.2 - - - +
615A GLU 4.1 5.2 - - - +
616A ASP* 1.4 85.8 - - + +
618A ASN* 1.3 74.2 + - - +
620A ALA* 3.2 17.0 + - - +
621A VAL* 3.4 15.1 - - + +
677A ARG* 3.6 42.4 - - + +
681A CYS* 5.1 9.6 - - - -
684A SER* 4.3 0.9 + - - -
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Residues in contact with ASN 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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616A ASP* 3.2 8.3 - - + +
617A PRO* 1.3 90.9 - - - +
619A ARG* 1.3 63.7 + - - +
621A VAL* 3.2 13.7 + - - +
622A HIS* 3.0 43.7 + - + +
676A ARG* 3.1 31.0 + - - +
677A ARG* 5.3 5.5 - - - +
680A LEU* 5.5 0.3 - - - +
703A ARG* 5.0 5.8 - - - +
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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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614A TYR* 4.8 10.3 - - + -
616A ASP* 3.2 36.1 + - - +
618A ASN* 1.3 78.0 - - - +
620A ALA* 1.3 62.9 + - - +
622A HIS* 3.4 7.7 + - - +
623A GLN* 3.0 26.1 + - - +
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Residues in contact with ALA 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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611A PRO* 3.7 26.2 - - + +
614A TYR* 3.8 22.1 - - + -
616A ASP 4.0 1.2 + - - -
617A PRO 3.2 12.2 + - - +
618A ASN 3.2 0.4 - - - -
619A ARG* 1.3 75.7 - - - +
621A VAL* 1.3 66.5 + - - +
623A GLN* 3.2 2.4 + - - -
624A PHE* 3.1 39.5 + - + +
684A SER* 3.4 13.2 + - - +
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Residues in contact with VAL 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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617A PRO* 3.4 15.3 - - + +
618A ASN* 3.2 16.1 + - - +
620A ALA* 1.3 77.3 - - - +
622A HIS* 1.3 62.2 + - + +
625A ALA* 3.0 39.6 + - + +
676A ARG* 6.0 0.4 - - - +
677A ARG* 5.6 0.9 - - - +
680A LEU* 3.9 35.9 - - + +
681A CYS* 4.9 1.6 - - - +
683A ALA* 5.1 0.9 - - + -
684A SER* 3.3 19.5 - - - +
700A VAL* 4.4 9.2 - - + -
702A THR* 4.0 27.8 - - + -
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Residues in contact with HIS 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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618A ASN* 3.0 36.6 + - + +
619A ARG* 3.4 6.5 + - - +
621A VAL* 1.3 79.9 - - + +
623A GLN* 1.3 61.1 + - - +
625A ALA 4.0 12.4 + - - +
627A GLU* 4.6 8.5 + - - +
676A ARG* 5.1 5.5 + - - -
700A VAL* 6.1 0.4 - - - +
702A THR* 3.7 30.0 - - + +
703A ARG* 5.8 3.5 + - + +
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Residues in contact with GLN 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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609A ILE* 5.0 4.9 - - - +
614A TYR* 2.6 38.5 + - - -
619A ARG 3.0 16.8 + - - +
620A ALA 3.2 4.5 + - - +
622A HIS* 1.3 79.4 - - - +
624A PHE* 1.3 83.3 + - + +
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Residues in contact with PHE 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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609A ILE* 4.3 11.9 - - + -
611A PRO* 5.6 0.2 - - + -
614A TYR* 3.7 23.8 - + - -
620A ALA* 3.1 30.1 + - + +
623A GLN* 1.3 116.2 - - + +
625A ALA* 1.3 60.0 + - - +
626A LYS 4.3 0.6 + - - -
684A SER* 3.6 26.5 - - - +
687A GLY* 3.3 31.1 - - - +
688A GLN* 3.5 40.8 - - + -
697A LEU* 4.1 0.7 - - - +
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Residues in contact with ALA 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A VAL* 3.0 23.4 + - + +
622A HIS* 4.0 12.4 + - - +
623A GLN 3.7 1.4 + - - -
624A PHE* 1.3 79.5 - - - +
626A LYS* 1.3 65.7 + - - +
627A GLU 3.4 2.6 + - - -
683A ALA* 4.0 14.8 - - + +
697A LEU* 3.8 21.8 - - + -
700A VAL* 3.7 24.0 - - + +
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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