Contacts of the strand formed by residues 57 - 62 (chain B) in PDB entry 5JSJ
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 ARG 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY 4.2 0.4 + - - -
56B CYS* 1.3 76.0 - - - +
58B ILE* 1.3 61.0 + - - +
73B LYS* 3.9 19.2 - - - +
74B GLY 3.2 10.0 + - - +
75B THR* 3.1 27.0 + - - +
92B ASP* 2.9 42.4 + - - -
113B VAL* 3.6 4.3 - - - -
114B LEU* 2.9 38.3 + - + +
116B ASP* 3.3 51.5 + - + +
117B ARG 5.2 0.4 - - - -
118B VAL* 4.0 24.9 - - + +
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Residues in contact with ILE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 4.6 15.3 - - + -
56B CYS* 4.4 2.0 - - + +
57B ARG* 1.3 79.3 - - - +
59B GLN* 1.3 61.0 + - - +
60B HIS* 4.0 17.7 - - + -
73B LYS* 3.4 4.3 - - - -
74B GLY* 2.8 41.9 + - - +
76B VAL* 3.9 22.9 - - + -
89B ILE* 4.8 7.9 - - + -
91B TYR* 5.2 0.9 - - + +
102B LEU* 3.6 29.6 - - + -
111B LEU* 3.7 21.1 - - + -
112B GLU 3.2 11.9 - - - +
113B VAL* 4.4 10.1 - - + -
114B LEU* 3.6 9.5 - - - +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 1.3 76.2 - - - +
60B HIS* 1.3 65.1 + - - +
71B GLN* 3.2 38.4 + - - +
72B TRP 3.2 12.3 - - - +
73B LYS* 3.6 31.6 + - + +
110B ALA 3.5 2.9 - - - +
111B LEU* 3.7 1.1 - - - +
112B GLU* 2.7 48.8 + - + +
114B LEU* 3.7 18.2 - - + +
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Residues in contact with HIS 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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58B ILE* 4.0 20.2 - - + -
59B GLN* 1.3 77.9 - - - +
61B GLY* 1.3 86.3 + - - +
62B TRP* 3.9 22.7 - + + -
70B THR 3.8 0.2 - - - +
71B GLN* 3.6 8.1 - - - +
72B TRP* 2.9 36.0 + - + +
91B TYR* 2.8 38.7 + + - -
100B LEU* 4.6 1.1 - - + -
102B LEU* 4.4 5.6 - - + +
108B VAL* 3.6 16.7 - - + +
109B SER 3.6 10.5 - - - +
110B ALA 3.9 4.0 - - - -
111B LEU* 3.7 15.5 - - + -
301B 6PD 3.9 9.4 - + - -
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Residues in contact with GLY 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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60B HIS* 1.3 91.5 + - - +
62B TRP* 1.3 61.2 + - - -
69B VAL* 4.0 7.2 - - - -
70B THR 3.2 8.5 - - - -
71B GLN* 4.1 8.3 + - - +
108B VAL* 3.5 2.1 - - - -
109B SER* 2.7 45.9 + - - -
110B ALA* 4.5 3.5 + - - +
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Residues in contact with TRP 62 (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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60B HIS* 3.9 4.7 - + + -
61B GLY* 1.3 74.4 - - - +
63B LYS* 1.3 64.1 + - - +
64B GLU* 3.9 22.2 + - + +
68B PRO 3.7 1.6 - - - +
69B VAL* 3.3 4.4 - - - +
70B THR* 2.7 46.4 + - - -
72B TRP* 3.5 28.9 - + + +
100B LEU* 3.5 26.9 - - + -
105B ASP* 3.9 5.4 - - - -
107B ARG* 3.4 66.0 - - + -
108B VAL* 3.7 17.9 - - + -
251B PHE* 4.4 8.8 - + - -
301B 6PD 3.3 32.0 - + - -
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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