Contacts of the helix formed by residues 617 - 630 (chain A) in PDB entry 4HDO
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 GLU 617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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615A SER* 3.3 11.1 - - - +
616A LYS* 1.3 77.8 - - - +
618A MET* 1.3 66.5 + - - +
619A HIS* 3.3 19.8 - - + -
620A HIS* 3.0 31.9 + - + +
621A LEU* 3.0 19.4 + - - +
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Residues in contact with MET 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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560A GLN 5.3 0.9 - - - +
561A ILE* 3.6 51.8 - - + +
616A LYS 3.4 4.8 + - - +
617A GLU* 1.3 72.1 + - - +
619A HIS* 1.3 59.1 + - - +
621A LEU* 3.2 8.7 + - + +
622A GLN* 2.9 54.7 + - - +
25B GLN 5.4 8.7 - - - +
26B GLY* 6.5 0.4 - - - -
42B LYS* 6.5 1.1 - - - -
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Residues in contact with HIS 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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523A GLU 4.1 19.9 + - - -
525A PRO* 4.1 35.4 - - + +
528A ILE* 3.6 15.6 - - + +
617A GLU* 4.1 23.2 - - + +
618A MET* 1.3 78.6 + - - +
620A HIS* 1.3 94.1 + + - +
622A GLN* 3.7 14.1 - - - +
623A ARG* 3.0 28.1 + - - +
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Residues in contact with HIS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A SER* 2.7 38.4 + - - +
617A GLU* 3.0 28.5 + - + +
619A HIS* 1.3 108.1 + + - +
621A LEU* 1.3 59.0 + - - +
623A ARG* 3.3 10.6 + - + +
624A MET* 3.0 34.4 + - + +
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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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557A LEU* 4.4 13.0 - - + +
560A GLN* 3.6 38.1 - - + +
561A ILE* 3.7 24.6 - - + +
608A LEU* 5.2 0.9 - - + -
614A VAL* 4.3 9.4 - - + -
615A SER 3.5 20.4 - - - +
616A LYS* 3.7 25.6 - - + +
617A GLU 3.0 9.6 + - - +
618A MET* 3.7 11.9 - - + +
620A HIS* 1.3 73.1 - - - +
622A GLN* 1.3 65.5 + - - +
624A MET* 3.2 21.5 + - - +
625A PHE* 3.0 21.3 + - - +
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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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525A PRO 4.6 0.5 - - - +
528A ILE* 3.6 15.7 - - + +
529A LEU* 3.6 32.3 - - - +
532A PHE* 3.7 40.2 - - + -
561A ILE* 4.1 6.6 - - + +
618A MET* 2.9 46.6 + - - +
619A HIS* 3.7 14.7 - - - +
621A LEU* 1.3 76.1 - - - +
623A ARG* 1.3 57.5 + - - +
625A PHE* 3.2 5.2 + - - +
626A LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 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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520A LYS 2.7 30.1 + - - -
521A GLN* 3.9 8.3 + - - +
522A ILE 3.5 24.7 + - - +
523A GLU* 5.0 10.7 + - - +
528A ILE* 3.9 19.9 - - + +
619A HIS 3.0 19.2 + - - +
620A HIS* 3.7 9.2 - - - +
621A LEU 3.2 0.2 - - - -
622A GLN* 1.3 74.0 - - - +
624A MET* 1.3 60.2 + - - +
626A LEU* 3.2 7.4 + - + +
627A GLN* 2.8 56.7 + - - +
630A TRP* 4.4 13.6 - - + -
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Residues in contact with MET 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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557A LEU* 3.8 23.3 - - + -
608A LEU* 4.2 14.6 - - + -
614A VAL* 4.0 25.4 - - + -
615A SER* 4.8 3.1 - - - +
620A HIS* 3.0 21.6 + - - +
621A LEU* 3.2 19.5 + - - +
623A ARG* 1.3 75.6 - - - +
625A PHE* 1.3 62.4 + - - +
627A GLN* 3.3 19.1 + - - +
628A ASN* 3.0 34.5 + - - +
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Residues in contact with PHE 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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532A PHE* 3.5 24.9 - + + -
535A ALA* 3.9 19.1 - - + -
536A ARG* 3.9 16.8 - - - -
539A LEU* 3.8 20.9 - - + -
554A LEU* 3.6 31.3 - - + +
557A LEU* 3.9 15.8 - - + +
558A LEU* 3.6 36.3 - - + -
561A ILE* 4.5 2.7 - - + -
621A LEU 3.0 12.5 + - - +
622A GLN 3.3 8.3 - - - +
623A ARG 3.2 0.2 - - - -
624A MET* 1.3 75.4 - - - +
626A LEU* 1.3 65.5 + - + +
628A ASN* 3.1 13.2 + - - +
629A CYS* 3.2 30.2 + - - -
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Residues in contact with LEU 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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519A GLU* 4.6 2.7 - - + +
528A ILE* 3.9 25.1 - - + +
531A LEU* 3.7 48.7 - - + +
532A PHE* 3.9 5.2 - - - +
535A ALA* 3.9 14.6 - - + -
622A GLN 3.0 18.0 + - - +
623A ARG* 3.2 9.8 + - + +
625A PHE* 1.3 75.7 - - + +
627A GLN* 1.3 59.6 + - - +
629A CYS* 2.8 20.2 + - - +
630A TRP* 3.0 38.3 + - + +
635A TYR* 3.8 20.6 - - + +
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Residues in contact with GLN 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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550A LYS* 5.4 0.2 + - - -
623A ARG* 2.8 45.9 + - + +
624A MET* 3.5 25.3 - - - +
625A PHE 3.3 0.2 - - - -
626A LEU* 1.3 72.8 - - - +
628A ASN* 1.3 62.1 + - - +
629A CYS 3.5 0.2 + - - -
630A TRP* 3.3 43.1 + - + +
631A GLU* 4.6 8.3 + - - +
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Residues in contact with ASN 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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550A LYS* 2.7 51.6 + - + +
553A THR* 4.0 19.0 - - - +
554A LEU* 3.5 16.4 - - + -
557A LEU* 3.6 17.2 - - - +
624A MET* 3.0 25.5 + - - +
625A PHE 3.1 9.4 + - - +
627A GLN* 1.3 77.3 - - - +
629A CYS* 1.3 60.4 + - - +
630A TRP 3.5 0.2 - - - -
631A GLU 4.5 0.6 + - - -
632A ILE* 4.0 3.8 - - - +
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Residues in contact with CYS 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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535A ALA* 4.2 2.9 - - - -
544A TYR* 3.9 24.2 - - + -
554A LEU* 4.0 13.2 - - - -
625A PHE* 3.2 41.8 + - - -
626A LEU* 2.8 9.9 + - - +
628A ASN* 1.3 75.6 - - - +
630A TRP* 1.3 63.8 + - - +
631A GLU 3.2 2.9 - - - -
632A ILE* 3.0 26.4 + - - +
635A TYR* 3.4 29.1 - - + +
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Residues in contact with TRP 630 (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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516A LEU* 3.7 21.4 - - + +
519A GLU* 2.9 40.4 + - + -
520A LYS* 3.6 47.8 - - + -
623A ARG* 4.4 13.7 - - + -
626A LEU* 3.0 41.1 + - + +
627A GLN* 3.3 43.2 + - + +
628A ASN 3.5 1.4 - - - -
629A CYS* 1.3 77.4 - - - +
631A GLU* 1.3 62.5 + - - +
632A ILE 4.0 0.2 - - - +
635A TYR* 3.6 28.9 - + - +
665A LYS* 2.5 32.2 + - - -
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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