Contacts of the helix formed by residues 518 - 526 (chain A) in PDB entry 2C3U
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 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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516A TRP 4.3 0.7 - - - -
517A SER* 1.3 79.9 - - - +
519A LEU* 1.3 59.7 + - - +
520A GLU* 3.0 22.8 - - - +
521A ASP* 2.5 29.3 + - - -
522A MET* 2.8 29.4 + - - +
616A PHE* 4.8 0.2 - - - -
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Residues in contact with LEU 519 (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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517A SER 3.9 2.0 + - - -
518A SER* 1.3 73.7 - - - +
520A GLU* 1.3 57.4 + - - +
522A MET* 4.3 4.3 - - - -
523A ASP* 3.0 46.1 + - - +
616A PHE* 4.1 21.9 - - + -
617A LYS 4.7 4.7 - - - +
619A PRO* 3.9 30.1 - - + -
622A TRP* 4.4 4.0 - - + -
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Residues in contact with GLU 520 (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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518A SER* 3.0 22.0 + - - +
519A LEU* 1.3 77.9 - - - +
521A ASP* 1.3 87.6 + - - +
523A ASP* 3.8 3.6 - - - +
524A LYS* 3.0 28.6 + - - +
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Residues in contact with ASP 521 (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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515A PRO 4.6 5.9 - - - +
516A TRP* 3.8 21.1 - - + -
518A SER* 2.5 28.1 + - - +
520A GLU* 1.3 89.5 - - - +
522A MET* 1.3 58.8 + - - +
524A LYS* 2.7 41.3 + - - +
525A HIS* 2.9 27.5 + - - +
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Residues in contact with MET 522 (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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512A LEU* 4.8 0.7 - - + -
514A SER* 4.3 0.9 - - - +
516A TRP* 3.0 46.1 - - + +
518A SER 2.8 19.9 + - - +
519A LEU 4.0 2.5 - - - +
521A ASP* 1.3 73.0 - - - +
523A ASP* 1.3 56.7 + - - +
526A LEU* 2.9 63.8 + - - +
531A LYS* 4.7 0.2 - - - -
541A PHE* 3.8 17.3 - - + -
543A ASN* 3.5 29.4 - - + +
616A PHE* 3.4 28.7 - - + -
622A TRP* 3.8 17.5 - - + -
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Residues in contact with ASP 523 (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 LEU* 3.0 34.2 + - - +
520A GLU* 3.8 4.3 - - - +
522A MET* 1.3 76.7 - - - +
524A LYS* 1.3 62.0 + - - +
526A LEU 3.7 3.7 - - - +
531A LYS* 2.7 37.2 + - - +
619A PRO* 5.0 2.8 - - - +
622A TRP* 2.7 37.9 + - - -
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Residues in contact with LYS 524 (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 GLU* 3.0 15.7 + - - +
521A ASP* 2.7 39.1 + - - +
523A ASP* 1.3 81.5 - - - +
525A HIS* 1.3 79.4 + - + +
526A LEU 4.5 1.2 - - - +
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Residues in contact with HIS 525 (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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495A VAL* 4.4 5.7 - - - +
516A TRP* 3.3 56.1 + + + -
521A ASP* 2.9 26.9 + - - +
524A LYS* 1.3 104.3 - - + +
526A LEU* 1.3 66.5 + - - +
527A PRO* 3.3 11.3 - - - +
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Residues in contact with LEU 526 (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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495A VAL* 3.4 29.8 - - + -
510A PHE* 5.5 0.7 - - + -
512A LEU* 4.6 8.1 - - + -
516A TRP* 4.5 3.5 - - + -
522A MET* 2.9 46.4 + - - +
523A ASP 3.7 5.2 - - - +
524A LYS 4.5 1.4 - - - +
525A HIS* 1.3 76.3 - - - +
527A PRO* 1.3 80.6 - - + +
530A ILE* 3.7 22.9 - - + -
531A LYS* 3.3 19.4 + - + -
534A ILE* 5.2 0.2 - - + -
541A PHE* 4.0 9.9 - - + -
622A TRP* 3.7 28.9 - - + -
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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