Contacts of the helix formed by residues 624 - 636 (chain A) in PDB entry 4CCZ
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 HIS 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A ASP 3.8 3.0 + - - -
623A ILE* 1.3 70.5 - - - +
625A LYS* 1.3 61.1 + - - +
626A GLU* 3.2 5.0 + - + +
627A LEU* 3.2 18.7 + - + +
628A LEU* 2.9 26.2 + - - +
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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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623A ILE 3.3 5.6 + - - +
624A HIS* 1.3 72.4 - - - +
626A GLU* 1.3 59.1 + - - +
628A LEU* 4.0 7.3 - - - +
629A GLN* 3.2 24.8 + - - +
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Residues in contact with GLU 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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624A HIS* 3.2 3.2 - - + +
625A LYS* 1.3 76.8 - - - +
627A LEU* 1.3 60.0 + - - +
629A GLN* 3.4 5.0 + - - +
630A LEU* 3.0 28.1 + - - +
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Residues in contact with LEU 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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589A ALA* 4.2 13.9 - - + +
590A ILE* 4.7 18.4 - - + -
593A ALA* 3.5 29.8 - - + -
623A ILE* 6.2 1.8 - - + -
624A HIS* 3.2 19.3 + - + +
626A GLU* 1.3 75.9 - - - +
628A LEU* 1.3 66.9 + - - +
630A LEU* 3.2 7.4 + - + +
631A CYS* 3.0 37.2 + - - -
646A LEU* 5.9 1.8 - - + +
649A TYR* 4.9 16.4 - - + -
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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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593A ALA* 6.2 0.4 - - - -
597A VAL* 3.9 22.3 - - + +
620A TYR* 3.3 61.7 - - + +
621A ASP* 5.5 0.4 - - - -
623A ILE* 3.8 20.1 - - + +
624A HIS 2.9 17.5 + - - +
625A LYS* 4.0 6.7 - - - +
627A LEU* 1.3 78.0 - - - +
629A GLN* 1.3 60.7 + - + +
631A CYS* 3.3 1.9 + - - +
632A GLU* 2.8 37.3 + - + +
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Residues in contact with GLN 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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625A LYS 3.2 18.3 + - - +
626A GLU* 3.8 4.5 - - - +
628A LEU* 1.3 83.4 - - + +
630A LEU* 1.3 61.3 + - - +
632A GLU* 3.5 9.3 - - - +
633A ASP* 3.2 21.8 + - - +
638A LYS* 5.9 0.2 + - - -
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Residues in contact with LEU 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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626A GLU 3.0 14.4 + - - +
627A LEU* 3.2 17.0 + - + +
629A GLN* 1.3 73.9 - - - +
631A CYS* 1.3 65.7 + - - +
633A ASP* 3.1 17.6 + - - +
634A LEU* 3.2 12.2 + - - +
642A ALA* 5.4 2.9 - - - +
645A LYS* 5.3 6.7 - - + +
646A LEU* 5.2 17.6 - - + +
649A TYR* 5.7 3.8 - - + -
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Residues in contact with CYS 631 (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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590A ILE* 4.6 5.2 - - - -
593A ALA* 4.3 4.7 - - - -
594A MET* 3.8 35.9 - - - -
597A VAL* 3.9 18.4 - - + -
627A LEU* 3.0 35.4 + - - +
628A LEU 3.8 3.1 - - - +
630A LEU* 1.3 72.9 - - - +
632A GLU* 1.3 66.0 + - - +
634A LEU* 2.9 9.8 + - - -
635A ILE* 2.9 36.7 + - + +
646A LEU* 6.1 4.7 - - - -
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Residues in contact with GLU 632 (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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597A VAL* 3.7 15.0 - - + +
601A HIS* 5.0 6.1 - - + -
620A TYR* 5.7 0.4 - - - +
628A LEU* 2.8 26.1 + - + +
629A GLN* 3.5 11.4 - - - +
631A CYS* 1.3 76.3 - - - +
633A ASP* 1.3 60.8 + - - +
635A ILE* 3.8 0.8 + - - +
636A TRP* 3.2 38.8 + - + +
638A LYS* 3.9 12.5 - - - +
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Residues in contact with ASP 633 (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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629A GLN 3.2 12.4 + - - +
630A LEU* 3.1 12.2 + - - +
631A CYS 3.1 0.8 - - - -
632A GLU* 1.3 75.3 - - - +
634A LEU* 1.3 59.4 + - - +
637A ASN* 2.9 24.1 + - - -
638A LYS* 3.2 25.2 + - + +
639A ASP* 4.0 24.9 + - + +
642A ALA* 4.0 5.7 - - + +
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Residues in contact with LEU 634 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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543A ILE* 3.7 26.7 - - + +
544A GLY* 4.2 23.6 - - - +
551A ASN 4.5 6.2 - - - +
594A MET* 4.0 31.6 - - + -
630A LEU 3.2 9.8 + - - +
631A CYS* 2.9 12.4 + - - +
633A ASP* 1.3 75.0 - - - +
635A ILE* 1.3 66.7 + - + +
637A ASN* 3.3 11.3 + - - +
642A ALA* 3.8 29.6 - - + +
643A THR* 4.5 6.5 - - - +
646A LEU* 4.5 16.8 - - + -
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Residues in contact with ILE 635 (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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543A ILE* 4.1 20.9 - - + -
551A ASN 4.5 4.9 - - - +
554A ALA* 3.7 22.3 - - + +
555A ILE* 3.8 11.3 + - - +
558A ILE* 4.0 17.7 - - + -
580A LEU* 4.5 6.3 - - + -
594A MET* 4.5 17.7 - - + +
597A VAL* 4.4 8.5 - - + -
598A PHE* 4.0 26.2 - - + -
601A HIS* 5.2 2.7 - - - +
631A CYS* 2.9 41.9 + - + +
632A GLU* 4.3 3.6 - - - +
634A LEU* 1.3 80.8 - - + +
636A TRP* 1.3 77.5 + - + +
637A ASN 3.4 0.7 + - - -
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Residues in contact with TRP 636 (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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555A ILE* 4.4 16.8 - - + -
558A ILE* 4.1 30.7 - - + -
559A HIS* 3.9 29.8 - + - -
601A HIS* 3.6 45.4 + + + -
632A GLU* 3.2 29.6 + - + +
635A ILE* 1.3 90.3 - - + +
637A ASN* 1.3 71.2 + - - +
638A LYS* 2.8 29.7 + - + +
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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