Contacts of the strand formed by residues 562 - 570 (chain A) in PDB entry 3F6K
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 SER 562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.8 20.0 + - - -
555A PHE* 4.7 8.2 - - - +
556A THR* 2.8 23.8 - - - -
557A GLU* 3.8 19.4 + - - -
561A THR* 1.3 81.9 - - - +
563A GLN* 1.3 66.7 + - - +
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Residues in contact with GLN 563 (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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71A VAL* 3.4 35.2 - - + +
72A PHE 4.5 7.4 - - - +
73A ASP* 5.9 1.8 - - - +
76A ARG* 4.4 6.9 - - - +
555A PHE* 3.2 6.5 - - - +
556A THR* 3.0 47.7 + - + +
562A SER* 1.3 82.1 + - - +
564A TRP* 1.3 69.2 + - - +
565A VAL* 3.8 2.2 + - + +
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Residues in contact with TRP 564 (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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71A VAL* 3.8 2.6 - - - -
72A PHE* 3.1 40.5 + - + +
74A ASP* 5.7 0.2 - - - -
75A LEU* 3.3 62.5 + - + -
76A ARG* 3.3 32.7 - - - +
77A GLY 5.6 1.6 - - - -
79A VAL* 5.0 7.0 - - + -
537A THR* 3.9 30.3 - - + -
553A TRP* 5.0 10.3 - + + -
554A GLY 3.5 18.2 - - - -
555A PHE* 4.2 19.5 - + + +
563A GLN* 1.3 77.2 - - - +
565A VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 565 (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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69A GLN* 3.7 18.2 - - + +
70A HIS 3.3 13.7 - - - +
71A VAL* 3.9 11.9 - - + -
72A PHE* 4.5 3.1 - - - -
534A ILE* 3.4 33.3 - - + +
552A ILE 3.9 0.5 - - - +
553A TRP* 3.7 4.5 - - - -
554A GLY 2.8 40.1 + - - +
555A PHE* 4.4 3.8 - - - -
556A THR* 4.6 4.5 - - + +
563A GLN* 4.5 6.1 - - + +
564A TRP* 1.3 77.2 - - - +
566A SER* 1.3 63.1 + - - +
567A TYR* 3.6 23.6 - - + +
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Residues in contact with SER 566 (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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68A HIS 4.2 0.4 + - - -
69A GLN* 3.3 2.9 - - - -
70A HIS* 2.8 43.4 + - - +
72A PHE* 3.4 18.9 - - - -
118A GLY 4.3 3.2 + - - -
121A PHE* 4.2 7.0 - - - -
551A SER* 5.0 4.3 - - - -
552A ILE 3.2 9.9 - - - -
553A TRP* 3.8 29.8 - - - -
565A VAL* 1.3 77.1 - - - +
567A TYR* 1.3 63.4 + - - +
568A THR* 4.1 2.5 - - - -
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Residues in contact with TYR 567 (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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67A THR* 4.2 15.0 - - + -
68A HIS 3.2 5.8 - - - +
69A GLN* 2.8 40.3 + - + -
529A PHE* 3.7 44.4 - + + -
530A THR* 2.6 18.3 + - - -
532A ASP* 2.6 28.9 + - - -
534A ILE* 4.2 16.2 - - + +
550A ILE 3.7 1.6 - - - +
551A SER* 3.4 1.1 - - - -
552A ILE* 2.8 43.6 + - + +
565A VAL* 3.6 23.5 - - + +
566A SER* 1.3 76.2 - - - +
568A THR* 1.3 61.3 + - - +
569A ILE* 4.1 0.6 + - + -
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Residues in contact with THR 568 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASN 3.4 2.4 - - - +
67A THR* 3.2 3.1 - - - -
68A HIS* 2.7 41.7 + - - +
117A TYR 3.4 20.0 - - - +
118A GLY 3.3 23.5 + - - -
119A LYS* 3.7 24.7 - - + -
549A ASN* 4.4 13.9 - - + -
550A ILE 3.4 11.9 - - - +
551A SER* 2.6 23.0 + - - +
566A SER* 4.1 2.1 - - - -
567A TYR* 1.3 72.0 - - - +
569A ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 569 (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 LEU* 3.6 30.1 - - + -
66A ASN 3.4 3.8 - - - +
67A THR* 3.9 22.4 - - + +
514A ILE* 4.0 24.7 - - + -
527A TYR* 4.1 5.8 - - + -
529A PHE* 4.0 15.0 - - + -
548A MET 3.6 2.3 - - - +
549A ASN* 3.3 5.5 - - - -
550A ILE* 2.9 41.5 + - + +
552A ILE* 3.6 29.8 - - + -
567A TYR* 4.7 1.1 - - + +
568A THR* 1.3 79.9 - - - +
570A ASP* 1.3 60.7 + - - +
571A PHE* 3.8 13.9 + - + -
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Residues in contact with ASP 570 (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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62A LYS 4.6 0.5 - - - +
63A LEU* 4.1 6.9 - - - +
66A ASN* 2.9 38.2 + - + +
119A LYS* 2.7 31.1 + - - +
548A MET* 3.6 12.3 - - - +
549A ASN* 3.1 19.2 - - - +
569A ILE* 1.3 73.3 - - - +
571A PHE* 1.3 61.0 + - - +
572A LYS* 3.1 44.5 + - - +
573A ASP 4.5 0.3 + - - -
1C NAG 3.8 12.2 + - - +
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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