Contacts of the strand formed by residues 482 - 487 (chain A) in PDB entry 6FF7
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 PHE 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 5.5 7.4 - - + -
120A TYR 3.2 11.9 - - - +
121A HIS* 4.7 0.9 - - - +
476A PHE* 3.3 35.7 - - + +
477A LYS* 4.0 11.6 - - - +
479A THR* 3.4 14.9 + - - +
480A LYS 3.4 2.8 - - - +
481A PHE* 1.3 77.7 - - - +
483A GLN* 1.3 60.7 + - - +
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Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL 4.0 0.3 - - - +
119A LEU* 3.3 5.0 - - - +
120A TYR* 2.9 34.4 + - + +
121A HIS 6.3 0.4 - - - -
122A ILE* 6.3 0.7 - - - +
481A PHE 5.6 0.9 - - - +
482A PHE* 1.3 75.4 - - - +
484A SER* 1.3 62.2 + - - +
485A THR* 4.1 1.9 + - - -
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Residues in contact with SER 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LYS 5.9 2.2 - - - -
59A GLU* 3.2 28.7 + - - +
60A ASP* 3.4 6.9 - - - -
61A MET* 4.0 3.6 + - - +
117A PRO* 6.5 0.4 - - - -
118A VAL 3.4 12.3 - - - -
119A LEU* 5.1 4.3 - - - -
477A LYS* 6.4 2.5 - - - -
483A GLN* 1.3 75.4 - - - +
485A THR* 1.3 61.1 + - - +
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 4.3 4.5 - - - +
61A MET* 4.3 27.4 - - - +
62A PRO 4.7 8.1 - - - -
63A PRO* 5.1 3.8 - - - -
65A HIS* 6.3 1.6 - - - -
117A PRO* 3.5 4.0 - - - +
118A VAL* 2.9 33.7 + - - +
483A GLN* 4.1 3.5 + - - -
484A SER* 1.3 75.3 - - - +
486A LYS* 1.3 61.4 + - - +
487A LEU* 4.1 2.0 - - - -
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Residues in contact with LYS 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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60A ASP* 4.6 13.0 - - + +
61A MET 4.8 3.6 + - - +
63A PRO* 3.3 19.3 - - - +
116A VAL 3.6 10.1 - - - +
117A PRO* 4.0 7.4 - - + -
485A THR* 1.3 74.3 - - - +
487A LEU* 1.3 59.4 + - - +
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Residues in contact with LEU 487 (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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63A PRO* 4.1 17.7 - - + +
66A VAL* 6.6 0.2 - - + -
115A ASP* 3.7 6.7 - - - +
116A VAL 2.9 34.8 + - - +
117A PRO 5.1 0.2 - - - -
118A VAL* 5.1 12.3 - - + -
485A THR* 4.1 2.8 + - - -
486A LYS* 1.3 73.4 - - - +
488A ASP* 1.3 68.1 + - - +
491A GLU* 5.0 7.9 - - + -
492A VAL* 5.6 4.3 - - + +
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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