Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 4JHN
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 LEU 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 4.2 3.6 - - + -
49B VAL 3.5 10.3 - - - +
50B VAL* 4.0 19.1 - - + -
55B LYS* 1.3 74.6 - - - +
57B TYR* 1.3 63.6 + - - +
58B MET* 3.9 21.3 - - - -
80B CYS* 3.3 7.0 - - - -
81B VAL* 2.9 53.9 + - + +
84B LEU* 3.8 14.1 - - + +
89B VAL* 4.1 17.7 - - + +
92B ALA* 4.0 14.6 - - + -
101B VAL* 3.6 24.7 - - + -
130B PHE* 3.9 9.9 - - + -
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Residues in contact with TYR 57 (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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32B PHE* 3.6 39.4 - + + +
35B ASP* 4.9 2.9 + - - -
47B SER 4.6 0.2 - - - -
48B ALA* 3.4 3.6 - - - -
49B VAL* 2.8 49.8 + - + +
51B THR* 3.7 24.7 - - + -
55B LYS* 3.8 32.3 + - + +
56B LEU* 1.3 76.9 - - - +
58B MET* 1.3 63.7 + - - +
59B PHE* 4.8 1.6 - - - -
78B PRO* 3.9 23.8 - - + -
79B THR 3.3 6.5 - - - +
80B CYS* 3.5 34.4 - - + +
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Residues in contact with MET 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.8 14.6 - - + -
47B SER 3.5 15.3 - - - +
48B ALA* 3.5 23.8 - - + -
56B LEU* 3.9 16.6 - - + -
57B TYR* 1.3 76.8 - - - +
59B PHE* 1.3 64.6 + - - +
66B GLN 3.9 8.1 - - - +
67B LEU* 3.3 34.3 - - + +
69B LEU* 4.2 6.3 - - + +
75B ILE* 4.4 1.9 - - - +
77B LYS 3.7 1.6 - - - +
79B THR* 2.9 32.1 + - - +
81B VAL* 3.7 16.6 - - + -
99B THR* 3.7 32.1 - - + +
130B PHE* 4.8 0.7 - - + -
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Residues in contact with PHE 59 (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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16B THR* 4.1 20.4 - - + -
20B SER* 3.6 25.4 - - - -
22B PHE* 4.2 6.1 - - + -
30B PHE* 4.0 29.8 - + - -
46B HIS* 3.5 3.5 - - - +
47B SER* 2.8 59.6 + - - +
49B VAL* 4.1 15.0 - - + -
57B TYR 4.8 0.9 - - - -
58B MET* 1.3 81.3 - - - +
60B GLY* 1.3 58.9 + - - +
67B LEU* 3.8 10.5 - - - +
75B ILE* 3.6 11.9 - - - +
76B SER 4.1 9.6 - - - +
77B LYS 3.6 14.6 - - - +
78B PRO* 3.8 15.7 - - + -
362B VAL* 4.3 5.8 - - + -
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Residues in contact with GLY 60 (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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20B SER 3.7 16.2 - - - -
21B LYS* 3.9 6.1 - - - -
45B GLU 3.6 9.2 - - - -
46B HIS* 4.1 0.4 - - - -
59B PHE* 1.3 76.2 - - - +
61B SER* 1.3 68.0 + - - +
67B LEU* 3.4 3.3 - - - +
74B ALA* 3.4 4.3 - - - -
75B ILE 2.8 37.5 + - - -
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Residues in contact with SER 61 (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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21B LYS* 5.1 0.6 - - - +
45B GLU* 2.9 46.9 + - - -
46B HIS* 3.7 1.6 - - - +
60B GLY* 1.3 73.3 - - - +
62B ASN* 1.3 60.8 + - - +
63B ASN* 3.2 21.7 + - - +
66B GLN* 3.2 26.2 + - - +
67B LEU* 3.6 7.8 - - - +
73B SER 4.1 6.8 + - - -
74B ALA* 4.2 5.2 - - - -
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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