Contacts of the strand formed by residues 480 - 486 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA 3.4 3.5 - - - +
10B ASN* 2.7 26.5 + - - +
71B HIS* 5.6 0.9 + - - -
82B TYR* 5.1 0.2 + - - -
418B GLN* 3.1 22.2 + - - -
419B ILE* 4.6 3.1 - - - +
454B LYS* 5.7 0.2 - - - +
457B PHE* 3.7 18.2 - - - +
458B ASN* 4.3 10.1 + - - +
475B CYS* 3.1 34.9 + - + +
477B GLN* 3.2 25.5 + - - +
478B PRO 3.2 10.7 + - - -
479B TYR* 1.3 76.9 - - - +
481B HIS* 1.3 68.2 + - - +
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Residues in contact with HIS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 3.9 1.2 - - - +
9B ALA* 2.7 39.1 + - + +
11B LEU* 3.6 27.6 - - + +
57B SER* 6.4 0.2 - - - -
58B ASN 5.8 0.2 - - - -
59B CYS* 4.1 0.4 - - - -
69B CYS* 3.4 29.7 - - + -
71B HIS* 5.3 3.8 - - - -
82B TYR* 2.8 24.8 + - - -
84B LEU* 3.9 12.4 - - + +
458B ASN* 4.9 1.4 - - - +
472B LEU* 4.2 13.1 - - + +
473B VAL 3.4 8.3 - - - +
474B ASN* 3.1 32.9 + - + -
475B CYS* 3.8 3.5 - - - -
480B ASN* 1.3 82.5 + - - +
482B SER* 1.3 67.0 + - - +
483B LEU 4.3 0.2 - - - -
610B PHE* 4.8 3.1 - - + -
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ARG* 3.5 20.5 + - - -
7B ILE 3.6 4.0 - - - -
8B ASP* 2.5 25.7 + - - -
458B ASN* 3.7 4.7 + - - -
472B LEU* 3.7 3.6 - - - -
473B VAL* 2.8 47.7 + - - +
475B CYS* 4.2 5.0 - - - -
481B HIS* 1.3 75.7 + - - +
483B LEU* 1.3 62.8 + - - +
484B TYR* 3.8 10.8 + - - -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER 3.7 0.2 - - - +
6B ARG* 3.7 1.4 - - - -
7B ILE* 2.8 46.7 + - + +
470B ILE* 3.4 27.4 - - + -
471B ILE 3.9 9.4 - - - +
472B LEU* 4.1 8.6 - - + +
482B SER* 1.3 73.4 - - - +
484B TYR* 1.3 64.6 + - - +
485B LYS* 3.5 33.5 + - + +
610B PHE* 4.4 12.6 - - + -
614B ILE* 3.8 41.1 - - + +
692B PHE* 4.7 8.3 - - + -
698B LEU* 4.4 9.2 - - + -
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Residues in contact with TYR 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.1 8.3 - - + +
5B SER 3.2 14.6 - - - -
6B ARG* 3.5 23.9 + - + -
354B LEU* 5.4 1.7 - - + +
361B SER* 3.6 19.1 + - - -
363B LEU* 3.9 26.7 - - + +
381B SER* 3.8 21.5 - - - -
382B VAL 3.5 20.9 - - - -
383B ASN* 3.7 12.1 + - - -
471B ILE* 3.2 25.5 + - + +
473B VAL* 3.8 27.1 - - + -
482B SER* 3.8 22.9 - - - -
483B LEU* 1.3 73.3 - - - +
485B LYS* 1.3 57.3 + - - +
695B TYR* 2.7 30.5 + - - -
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Residues in contact with LYS 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.3 2.9 - - - -
5B SER* 2.8 39.1 + - - +
7B ILE* 4.0 9.9 - - + -
483B LEU* 3.5 16.5 + - + +
484B TYR* 1.3 73.5 - - - +
486B LEU* 1.3 84.3 + - - +
487B ASN* 3.3 2.8 + - - +
488B THR* 4.1 9.9 - - - +
491B GLU* 2.6 35.0 + - - -
618B SER* 4.0 25.4 - - - +
621B GLN* 3.6 20.2 - - - +
695B TYR* 3.9 3.8 - - + -
698B LEU* 3.6 29.4 - - + -
699B ILE* 4.6 8.9 - - + +
702B ILE* 5.4 5.3 - - + +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B CYS* 3.8 15.5 - - + +
4B LEU* 4.2 7.4 - - + +
340B LEU* 4.7 7.6 - - + -
341B GLU* 3.7 50.0 - - + +
342B LEU* 4.4 21.1 - - + -
343B ASN* 5.3 2.9 - - - +
484B TYR 4.0 0.2 + - - -
485B LYS* 1.3 94.3 + - - +
487B ASN* 1.3 69.4 + - - +
695B TYR* 3.6 39.0 - - + -
699B ILE* 4.0 17.2 - - + +
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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