Contacts of the strand formed by residues 56 - 63 (chain K) in PDB entry 2JA7
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 VAL 56 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H PRO* 5.1 5.9 - - - +
50K LEU* 3.5 37.2 - - + +
51K LEU* 4.8 12.1 - - + +
53K ASP* 2.6 38.2 + - + +
54K ARG* 4.5 4.5 - - - +
55K LYS* 1.3 70.5 - - - +
57K LEU* 1.3 61.5 + - - +
58K PHE* 3.4 23.1 - - - +
59K ALA* 4.1 6.5 - - + -
75K ILE* 4.5 1.3 - - + -
76K GLN 3.3 13.0 - - - +
77K THR* 3.6 17.9 - - + -
86K ALA* 4.1 4.3 - - + -
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Residues in contact with LEU 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A LEU* 5.2 2.6 - - - +
560A ILE* 3.8 16.1 - - + +
79H TRP 5.7 0.2 - - - +
80H ARG* 3.8 46.2 - - + +
81H PRO* 4.2 25.9 - - + +
83H GLN* 5.2 6.3 - - - +
51K LEU* 6.0 0.7 - - - -
54K ARG 5.9 1.8 - - - +
55K LYS 3.5 2.4 + - - +
56K VAL* 1.3 73.0 - - - +
58K PHE* 1.3 61.3 + - - +
76K GLN* 2.6 35.4 + - + +
77K THR 3.2 30.3 - - - +
78K THR* 3.8 12.6 - - + +
79K GLU 5.4 0.2 - - - +
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Residues in contact with PHE 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 3.1 62.6 - - + -
550A LEU* 5.2 0.2 - - + -
551A TYR* 4.4 4.5 - - + -
556A TRP* 4.0 16.4 - + - -
560A ILE* 4.4 8.3 - - + -
51K LEU* 5.4 1.6 - - - -
56K VAL* 3.3 7.4 - - - +
57K LEU* 1.3 80.6 - - - +
59K ALA* 1.3 75.4 + - - +
60K ALA* 3.5 20.6 - - + -
74K ARG* 2.9 57.0 - - + -
75K ILE* 3.4 0.9 - - - -
76K GLN* 2.7 50.5 + - + +
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Residues in contact with ALA 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU* 3.8 16.1 - - - +
47K ARG* 3.0 27.5 + - + +
50K LEU* 4.4 25.8 - - + +
51K LEU* 4.8 7.2 - - + +
56K VAL* 4.1 12.6 - - + -
58K PHE* 1.3 87.2 - - - +
60K ALA* 1.3 62.8 + - - +
73K LEU* 5.1 0.9 - - + -
74K ARG 3.1 11.4 - - - +
75K ILE* 4.7 0.4 - - - -
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Residues in contact with ALA 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A LEU 3.6 0.9 - - - +
548A ASN* 3.1 38.4 - - - +
551A TYR* 3.9 10.3 - - + -
47K ARG* 3.8 7.8 - - - +
58K PHE* 3.5 20.9 - - + -
59K ALA* 1.3 73.7 - - - +
61K TYR* 1.3 57.3 + - - +
73K LEU* 2.7 23.6 - - - +
74K ARG* 2.9 15.6 + - - +
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Residues in contact with TYR 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A ASN* 2.7 28.8 + - - +
551A TYR* 4.1 3.5 - - - -
552A TRP* 4.3 3.3 + - - -
655A PHE* 5.9 4.4 - + - -
1076B HIS* 4.9 1.7 - - - +
1077B THR* 5.8 0.7 - - - +
40K HIS* 2.5 45.3 + + - -
43K GLY* 3.1 27.4 - - - +
44K ASN* 3.0 37.3 - - - +
47K ARG* 4.2 8.3 - - + -
60K ALA* 1.3 75.7 - - - +
62K LYS* 1.3 69.9 + - - +
63K VAL* 5.5 1.1 - - + -
71K PHE* 3.9 17.3 - + + -
72K LYS 3.2 13.9 - - - +
73K LEU* 3.6 15.9 - - + -
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Residues in contact with LYS 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A TYR* 3.3 59.7 + - + -
552A TRP* 3.2 45.8 + - + +
554A PRO* 5.0 9.3 - - - +
61K TYR* 1.3 84.6 - - - +
63K VAL* 1.3 61.5 + - - +
64K GLU* 3.7 32.0 + - - +
71K PHE* 3.0 21.1 - - - +
72K LYS* 2.9 26.4 + - + +
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Residues in contact with VAL 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A TRP* 3.7 24.0 - - + -
1076B HIS* 5.7 0.4 - - - +
39K ASP* 5.1 4.7 - - + -
40K HIS* 3.7 50.8 - - + +
61K TYR* 5.4 1.6 - - + +
62K LYS* 1.3 74.0 - - - +
64K GLU* 1.3 66.0 + - - +
65K HIS* 4.7 7.9 - - - +
66K PRO* 5.1 11.0 - - + -
68K PHE 5.5 3.6 - - - +
70K ARG 3.9 15.7 - - - +
71K PHE* 4.3 6.7 - - + -
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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