Contacts of the strand formed by residues 480 - 486 (chain C) in PDB entry 3F7F
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 ASN 480 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ALA 3.3 3.5 - - - +
10C ASN* 2.7 24.9 + - - +
71C HIS* 5.6 0.9 + - - -
82C TYR* 5.1 0.2 + - - -
418C GLN* 3.2 22.3 + - - +
419C ILE* 4.7 3.3 - - - +
457C PHE* 3.7 19.4 - - - +
458C ASN* 4.3 9.7 + - - +
475C CYS* 3.1 33.6 + - + +
477C GLN* 3.2 31.9 + - - +
478C PRO 3.2 6.1 + - - -
479C TYR* 1.3 77.2 - - - +
481C HIS* 1.3 68.6 + - - +
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Residues in contact with HIS 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASP* 3.8 1.4 - - - +
9C ALA* 2.7 39.3 + - + +
11C LEU* 3.6 28.1 - - + +
58C ASN 5.8 0.2 - - - -
59C CYS* 4.1 0.7 - - - -
69C CYS* 3.4 29.0 - - + -
71C HIS* 5.3 4.5 - - - -
82C TYR* 2.7 23.8 + - - -
84C LEU* 3.9 11.6 - - + +
458C ASN* 5.0 1.2 - - - +
472C LEU* 4.2 13.3 - - + +
473C VAL 3.4 8.7 - - - +
474C ASN* 3.1 32.3 + - + -
475C CYS* 3.7 3.7 - - - -
479C TYR 4.1 0.2 - - - -
480C ASN* 1.3 83.1 + - - +
482C SER* 1.3 65.9 + - - +
483C LEU 4.3 0.4 - - - -
610C PHE* 4.7 2.7 - - + -
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Residues in contact with SER 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.5 21.2 + - - -
7C ILE 3.7 4.0 - - - -
8C ASP* 2.5 25.9 + - - -
458C ASN* 3.7 4.7 + - - -
472C LEU* 3.7 4.4 - - - -
473C VAL* 2.8 48.7 + - - +
475C CYS* 4.2 5.6 - - - -
481C HIS* 1.3 75.3 + - - +
483C LEU* 1.3 61.3 + - - +
484C TYR* 3.8 10.4 + - - -
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Residues in contact with LEU 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.7 1.4 - - - -
7C ILE* 2.8 46.3 + - + +
466C TYR* 6.0 0.2 - - + -
470C ILE* 3.4 26.7 - - + -
471C ILE 3.9 11.0 - - - +
472C LEU* 4.1 8.6 - - + +
481C HIS 4.3 0.4 - - - -
482C SER* 1.3 72.3 - - - +
484C TYR* 1.3 65.3 + - - +
485C LYS* 3.5 33.6 + - + +
610C PHE* 4.4 12.3 - - + -
614C ILE* 3.9 40.4 - - + +
692C PHE* 4.7 8.3 - - + -
698C LEU* 4.4 8.7 - - + -
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Residues in contact with TYR 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.0 9.1 - - + +
5C SER 3.2 13.0 - - - -
6C ARG* 3.5 24.7 + - + -
354C LEU* 5.4 1.0 - - + +
361C SER* 3.6 19.4 + - - -
363C LEU* 3.8 31.4 - - + +
381C SER* 3.8 14.8 - - - -
382C VAL 3.5 21.8 - - - -
383C ASN* 3.7 11.8 + - - -
471C ILE* 3.2 25.7 + - + +
473C VAL* 3.8 26.9 - - + -
482C SER* 3.8 22.7 - - - -
483C LEU* 1.3 73.4 - - - +
485C LYS* 1.3 58.1 + - - +
695C TYR* 2.7 30.3 + - - -
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Residues in contact with LYS 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.2 2.8 - - - -
5C SER* 2.7 40.6 + - - +
7C ILE* 4.0 9.4 - - + -
483C LEU* 3.5 16.5 + - + +
484C TYR* 1.3 73.7 - - - +
486C LEU* 1.3 84.7 + - - +
487C ASN* 3.3 2.9 - - - +
488C THR* 4.1 9.5 - - - +
491C GLU* 2.6 34.0 + - - -
618C SER* 4.0 25.8 - - - +
621C GLN* 3.6 20.2 - - - +
695C TYR* 3.9 3.6 - - + -
698C LEU* 3.6 28.5 - - + -
699C ILE* 4.6 7.7 - - + +
702C ILE* 5.4 6.0 - - + +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C CYS* 3.7 14.8 - - + +
4C LEU* 4.2 7.8 - - + +
340C LEU* 4.7 7.6 - - + -
341C GLU* 3.7 50.0 - - + +
342C LEU* 4.4 21.8 - - + -
343C ASN* 5.3 2.9 - - - +
484C TYR 4.0 0.2 + - - -
485C LYS* 1.3 93.6 + - - +
487C ASN* 1.3 69.5 + - - +
488C THR 3.9 0.2 + - - -
695C TYR* 3.6 38.7 - - + -
699C ILE* 4.0 17.1 - - + +
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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