Contacts of the strand formed by residues 480 - 486 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA 3.3 3.7 - - - +
10A ASN* 2.7 26.0 + - - +
71A HIS* 5.5 0.7 + - - -
82A TYR* 5.1 0.2 + - - -
418A GLN* 3.1 22.0 + - - -
419A ILE* 4.7 3.1 - - - +
454A LYS* 5.7 0.2 - - - +
457A PHE* 3.7 18.4 - - - +
458A ASN* 4.3 9.8 + - - +
475A CYS* 3.1 34.9 + - + +
477A GLN* 3.2 30.8 + - - +
478A PRO 3.2 5.5 + - - -
479A TYR* 1.3 76.9 + - - +
481A HIS* 1.3 68.7 + - - +
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Residues in contact with HIS 481 (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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8A ASP* 3.9 1.0 - - - +
9A ALA* 2.7 39.5 + - + +
11A LEU* 3.6 27.6 - - + +
58A ASN 5.9 0.2 - - - -
59A CYS* 4.1 0.4 - - - -
69A CYS* 3.4 29.0 - - + -
71A HIS* 5.3 4.0 - - - -
82A TYR* 2.8 25.0 + - - -
84A LEU* 3.9 12.6 - - + +
458A ASN* 5.0 1.4 - - - +
472A LEU* 4.2 13.1 - - + +
473A VAL 3.4 8.1 - - - +
474A ASN* 3.1 32.7 + - + -
475A CYS* 3.7 3.5 - - - -
479A TYR 4.1 0.2 - - - -
480A ASN* 1.3 82.7 + - - +
482A SER* 1.3 66.8 + - - +
483A LEU 4.3 0.2 - - - -
610A PHE* 4.8 2.9 - - + -
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Residues in contact with SER 482 (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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6A ARG* 3.5 16.5 + - - -
7A ILE 3.6 4.3 - - - -
8A ASP* 2.5 25.5 + - - -
458A ASN* 3.7 9.0 + - - -
472A LEU* 3.8 2.2 - - - -
473A VAL* 2.8 48.2 + - - +
475A CYS* 4.2 5.2 - - - -
481A HIS* 1.3 76.1 + - - +
483A LEU* 1.3 63.6 + - - +
484A TYR* 3.7 11.0 + - - -
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Residues in contact with LEU 483 (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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5A SER 3.7 0.2 - - - +
6A ARG* 3.7 1.4 - - - -
7A ILE* 2.8 47.4 + - + +
470A ILE* 3.4 27.4 - - + -
471A ILE 3.9 9.0 - - - +
472A LEU* 4.1 8.6 - - + +
482A SER* 1.3 73.3 - - - +
484A TYR* 1.3 64.2 + - - +
485A LYS* 3.5 33.7 + - + +
610A PHE* 4.4 12.6 - - + -
614A ILE* 3.8 40.9 - - + +
692A PHE* 4.7 8.3 - - + -
698A LEU* 4.4 9.4 - - + -
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Residues in contact with TYR 484 (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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4A LEU* 4.1 8.5 - - + +
5A SER 3.2 14.4 - - - -
6A ARG* 3.6 24.6 + - + -
354A LEU* 5.4 1.6 - - + +
361A SER* 3.6 19.6 + - - -
363A LEU* 3.8 25.6 - - + +
381A SER* 3.8 21.8 - - - -
382A VAL 3.5 21.1 - - - -
383A ASN* 3.7 11.6 + - - -
471A ILE* 3.2 25.9 + - + +
473A VAL* 3.8 26.7 - - + -
482A SER* 3.8 22.4 - - - -
483A LEU* 1.3 73.5 - - - +
485A LYS* 1.3 58.0 + - - +
695A TYR* 2.7 30.5 + - - -
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Residues in contact with LYS 485 (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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4A LEU* 3.2 2.8 - - - -
5A SER* 2.7 39.3 + - - +
7A ILE* 4.0 9.6 - - + -
483A LEU* 3.5 16.5 + - + +
484A TYR* 1.3 72.5 - - - +
486A LEU* 1.3 83.3 + - - +
487A ASN* 3.3 2.8 + - - +
488A THR* 4.1 9.7 - - - +
491A GLU* 2.6 35.4 + - - -
618A SER* 4.0 25.4 - - - +
621A GLN* 3.6 20.4 - - - +
695A TYR* 3.9 3.6 - - + -
698A LEU* 3.7 29.2 - - + -
699A ILE* 4.6 8.9 - - + +
702A ILE* 5.4 5.1 - - + +
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Residues in contact with LEU 486 (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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3A CYS* 3.8 15.3 - - + +
4A LEU* 4.2 7.8 - - + +
340A LEU* 4.7 7.4 - - + -
341A GLU* 3.7 49.8 - - + +
342A LEU* 4.4 22.0 - - + -
343A ASN* 5.3 2.7 - - - +
484A TYR 4.0 0.2 + - - -
485A LYS* 1.3 93.8 + - - +
487A ASN* 1.3 69.7 + - - +
695A TYR* 3.6 39.0 - - + -
699A ILE* 4.0 16.8 - - + +
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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