Contacts of the helix formed by residues 501 - 507 (chain A) in PDB entry 3L6X
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 VAL 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460A LEU* 4.2 17.7 - - + -
469A THR* 4.2 22.9 - - + -
473A THR* 4.4 4.0 - - + -
497A LEU* 3.2 14.0 + - - +
499A ASP 3.5 0.6 - - - -
500A GLU* 1.3 86.7 - - + +
502A ILE* 1.3 68.4 + - - +
503A ILE 3.4 1.1 - - - -
504A PRO* 3.5 1.3 - - - -
505A HIS* 3.1 33.2 + - + +
526A VAL* 3.5 19.5 - - + -
527A LEU* 3.8 10.4 - - + +
530A THR* 3.3 31.9 - - + +
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Residues in contact with ILE 502 (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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497A LEU 3.0 15.0 + - - +
498A THR* 3.8 13.5 - - + +
501A VAL* 1.3 76.1 - - - +
503A ILE* 1.3 61.4 + - + +
506A SER* 2.9 35.3 + - - -
527A LEU* 4.0 18.3 - - + +
530A THR* 3.6 31.0 - - + -
531A ALA* 4.5 9.0 - - + +
534A LEU* 4.5 4.9 - - + -
554A LEU* 4.3 22.9 - - + -
557A ALA* 3.6 23.8 - - + -
558A LEU* 4.7 14.6 - - + -
561A ILE* 4.5 12.3 - - + -
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Residues in contact with ILE 503 (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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498A THR* 2.9 29.1 + - + +
499A ASP* 3.7 17.0 - - - +
502A ILE* 1.3 77.7 - - - +
504A PRO* 1.3 72.1 - - + +
506A SER* 3.0 18.7 + - - -
507A GLY 4.2 1.6 + - - -
508A TRP* 4.0 38.8 - - + +
552A ASP* 3.6 24.2 - - - +
553A GLY* 4.1 13.2 - - - +
557A ALA* 4.6 3.4 - - + -
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Residues in contact with PRO 504 (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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499A ASP 3.2 28.3 - - - +
500A GLU* 3.3 18.2 - - - +
501A VAL 3.3 13.5 - - - +
503A ILE* 1.3 97.9 - - + +
505A HIS* 1.3 68.2 + - + +
507A GLY* 4.1 5.7 + - - -
520A HIS 5.2 0.9 - - - +
522A GLU* 4.1 6.3 - - - +
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Residues in contact with HIS 505 (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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469A THR* 5.7 0.2 - - - +
500A GLU 3.9 9.8 + - - -
501A VAL* 3.1 40.8 + - + +
504A PRO* 1.3 81.4 - - + +
506A SER* 1.3 64.6 + - - +
507A GLY 3.3 3.4 + - - -
520A HIS 3.8 0.4 - - - +
521A ILE* 3.5 0.9 - - - -
522A GLU* 2.6 70.1 + - + +
523A TRP* 3.2 53.8 - + + -
526A VAL* 4.9 0.2 - - + -
527A LEU* 3.8 12.6 - - + +
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Residues in contact with SER 506 (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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502A ILE 2.9 17.5 + - - -
503A ILE* 3.0 14.0 + - - -
505A HIS* 1.3 78.6 - - - +
507A GLY* 1.3 56.6 + - - +
508A TRP* 2.9 25.5 + - - +
521A ILE* 3.5 18.5 - - - +
527A LEU* 4.3 2.6 - - - +
557A ALA* 3.9 9.5 - - - +
560A PHE* 3.3 15.8 - - - -
561A ILE* 3.7 30.2 - - - +
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Residues in contact with GLY 507 (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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503A ILE 4.2 0.4 + - - -
504A PRO 4.1 6.4 + - - -
505A HIS 3.3 3.4 - - - -
506A SER* 1.3 77.6 + - - +
508A TRP* 1.3 63.8 + - - +
509A GLU* 3.8 13.5 + - - +
520A HIS* 3.5 34.2 + - - -
521A ILE 3.8 0.2 - - - -
560A PHE* 3.5 16.9 - - - -
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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