Contacts of the helix formed by residues 615 - 629 (chain A) in PDB entry 4CCN
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 SER 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A CYS* 3.9 0.5 - - - +
614A ASP* 1.3 81.0 - - - +
616A VAL* 1.3 76.4 + - - +
617A GLU* 3.4 12.1 + - - +
618A ASP* 3.4 24.8 + - - +
619A GLN* 3.1 24.6 + - - +
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Residues in contact with VAL 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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544A THR* 3.7 28.0 - - + -
615A SER* 1.3 83.0 + - - +
617A GLU* 1.3 74.3 + - + +
618A ASP 3.1 0.2 - - - -
619A GLN* 3.1 15.9 + - - +
620A LEU* 3.1 32.3 + - + +
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Residues in contact with GLU 617 (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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615A SER* 3.4 8.2 + - - +
616A VAL* 1.3 86.0 - - + +
618A ASP* 1.3 62.6 + - - +
620A LEU* 4.0 8.9 - - - +
621A SER* 2.8 32.4 + - - -
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Residues in contact with ASP 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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590A GLN* 4.5 24.3 - - - +
591A GLN* 3.7 8.4 + - + +
613A CYS* 3.7 26.3 - - + -
614A ASP* 4.4 5.7 - - - +
615A SER* 3.4 28.7 + - - +
616A VAL 3.1 0.8 - - - -
617A GLU* 1.3 78.0 - - - +
619A GLN* 1.3 63.7 + - - +
620A LEU 3.4 0.2 - - - -
621A SER* 3.1 17.1 + - - -
622A LEU* 3.4 15.9 + - - +
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Residues in contact with GLN 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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544A THR* 4.6 1.8 - - + +
608A VAL* 3.3 23.7 - - + +
609A GLY* 3.4 23.4 + - - +
611A LEU* 2.7 46.8 + - + +
613A CYS* 3.8 21.3 - - + -
615A SER 3.1 15.2 - - - +
616A VAL* 3.1 25.8 + - - +
618A ASP* 1.3 77.7 - - - +
620A LEU* 1.3 63.3 + - + +
623A ALA* 3.3 24.6 + - - +
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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
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542A LEU* 4.0 11.4 - - + +
543A THR* 3.7 15.0 - - - +
544A THR* 3.7 36.1 - - + +
608A VAL* 4.3 6.1 - - + -
616A VAL* 3.1 37.1 + - + +
617A GLU* 4.0 7.0 - - - +
619A GLN* 1.3 77.5 - - - +
621A SER* 1.3 58.1 + - - +
623A ALA* 3.8 1.5 - - - +
624A THR* 2.7 40.7 + - - +
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Residues in contact with SER 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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591A GLN* 3.1 17.4 + - - -
617A GLU 2.8 21.4 + - - -
618A ASP* 3.1 9.7 + - - -
620A LEU* 1.3 77.6 - - - +
622A LEU* 1.3 60.3 + - - +
624A THR* 3.7 4.0 - - - -
625A THR* 2.7 42.6 + - - -
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Residues in contact with LEU 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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585A LEU* 6.0 0.2 - - + -
587A ILE* 4.2 15.9 - - + -
591A GLN* 3.6 25.5 - - + +
594A ALA* 3.6 33.0 - - + -
595A MET* 4.0 21.8 - - + +
598A LEU* 4.3 7.9 - - + -
611A LEU* 4.3 9.4 - - + -
613A CYS* 4.8 0.9 - - - -
618A ASP 3.4 14.7 + - - +
619A GLN 4.1 2.7 - - - +
621A SER* 1.3 80.4 + - - +
623A ALA* 1.3 55.2 + - - +
625A THR* 3.2 6.8 + - + -
626A LEU* 2.8 63.0 + - + +
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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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542A LEU* 3.5 22.2 - - + +
548A VAL* 5.3 0.7 - - + -
598A LEU* 6.0 1.1 - - - -
608A VAL* 3.8 21.8 - - + -
611A LEU* 5.0 4.2 - - + +
619A GLN 3.3 17.9 + - - +
620A LEU* 3.8 3.1 - - - +
622A LEU* 1.3 81.2 - - - +
624A THR* 1.3 57.7 + - - +
626A LEU* 3.8 2.4 - - - +
627A TYR* 2.8 32.9 + - - +
632A LEU* 3.9 12.7 - - + +
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Residues in contact with THR 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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542A LEU* 4.1 22.9 + - + +
620A LEU* 2.7 31.4 + - - +
621A SER* 3.7 4.9 - - - -
623A ALA* 1.3 72.7 - - - +
625A THR* 1.3 66.3 + - - +
627A TYR* 4.4 3.8 - - - -
628A ASP* 2.9 47.6 + - - +
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Residues in contact with THR 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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585A LEU* 4.4 27.1 - - + -
591A GLN* 5.9 0.2 + - - -
621A SER* 2.7 28.8 + - - -
622A LEU* 3.6 7.2 - - + -
624A THR* 1.3 74.6 - - - +
626A LEU* 1.3 64.3 + - + +
628A ASP* 3.5 5.8 + - - +
629A LYS* 3.2 22.9 + - + +
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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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550A MET* 3.9 13.2 - - + -
567A LEU* 3.6 31.4 - - + -
585A LEU* 4.9 8.5 - - + -
595A MET* 3.9 10.5 - - - -
598A LEU* 3.8 22.9 - - + -
622A LEU* 2.8 50.2 + - + +
623A ALA 3.8 2.7 - - - +
625A THR* 1.3 73.9 - - + +
627A TYR* 1.3 64.3 + - - +
629A LYS* 3.0 14.8 + - - +
630A GLY 3.3 0.2 + - - -
631A LEU* 3.2 30.7 + - + +
632A LEU* 4.1 15.5 - - + -
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Residues in contact with TYR 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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521A LEU 3.9 18.0 + - - -
522A SER* 3.3 17.2 + - - -
523A VAL* 3.5 37.1 + - + +
526A LEU* 3.4 28.4 - - + +
542A LEU* 3.8 25.8 - - + -
623A ALA 2.8 22.4 + - - +
624A THR 3.7 2.5 - - - +
626A LEU* 1.3 73.3 - - - +
628A ASP* 1.3 70.8 - - - +
630A GLY* 2.9 18.0 + - - -
632A LEU* 3.6 28.3 - - + +
634A THR* 4.2 14.8 + - + -
638A LEU* 3.5 25.7 + - + +
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Residues in contact with ASP 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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523A VAL* 4.3 16.8 - - + +
542A LEU* 5.8 0.2 - - - +
624A THR* 2.9 39.0 + - - +
625A THR* 3.9 5.6 - - - +
627A TYR* 1.3 90.1 - - - +
629A LYS* 1.3 62.1 + - - +
630A GLY 3.2 1.0 + - - -
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Residues in contact with LYS 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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523A VAL* 5.0 0.2 - - - -
524A TYR* 3.9 2.3 + - - -
569A TYR* 3.0 38.6 - - + +
571A VAL* 3.7 15.2 - - - +
572A GLU* 3.7 22.2 + - - +
585A LEU* 3.8 20.9 - - + -
625A THR* 3.2 12.4 + - + +
626A LEU 3.0 10.8 + - - +
628A ASP* 1.3 78.4 + - - +
630A GLY* 1.3 62.8 + - - +
631A LEU* 3.7 14.1 - - + +
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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