Contacts of the strand formed by residues 70 - 79 (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 THR 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLY* 3.2 6.3 - - - -
62B TRP* 2.7 51.1 + - - +
68B PRO* 3.9 18.2 - - + +
69B VAL* 1.3 79.1 - - - +
71B GLN* 1.3 61.7 + - - +
72B TRP* 2.8 33.1 + - + -
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Residues in contact with GLN 71 (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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59B GLN* 3.2 43.4 + - - +
60B HIS* 3.6 13.6 - - - +
61B GLY* 4.1 8.5 + - - +
69B VAL* 5.4 4.4 - - - +
70B THR* 1.3 75.2 + - - +
72B TRP* 1.3 68.6 + - - +
110B ALA* 5.4 4.1 - - - +
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Residues in contact with TRP 72 (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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59B GLN* 3.2 5.9 - - - +
60B HIS* 2.9 39.9 + + - +
62B TRP* 3.5 29.6 - + + +
70B THR* 2.8 31.3 + - + -
71B GLN* 1.3 84.2 - - - +
73B LYS* 1.3 62.8 + - - +
91B TYR* 3.9 27.1 - + + -
92B ASP 5.9 0.7 - - - -
94B PHE* 3.8 28.3 - + - -
301B 6PD 3.5 55.0 - + + -
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Residues in contact with LYS 73 (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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57B ARG* 3.9 18.2 - - - +
58B ILE 3.4 10.5 - - - +
59B GLN* 3.6 34.8 + - + +
71B GLN* 6.3 0.2 - - + -
72B TRP* 1.3 76.3 - - - +
74B GLY* 1.3 58.2 + - - +
91B TYR* 3.4 10.4 - - - +
92B ASP* 2.9 43.2 + - + +
114B LEU* 4.1 15.9 - - + +
116B ASP* 6.0 0.2 - - - +
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Residues in contact with GLY 74 (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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57B ARG* 3.2 9.6 + - - +
58B ILE* 2.8 38.5 + - - +
73B LYS* 1.3 78.1 - - - +
75B THR* 1.3 62.4 + - - -
89B ILE* 4.2 5.8 - - - -
90B LYS 3.2 12.1 - - - -
91B TYR* 4.0 10.0 - - - -
92B ASP* 3.9 3.5 + - - -
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Residues in contact with THR 75 (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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56B CYS 3.9 9.2 - - - +
57B ARG* 3.1 25.9 + - + +
74B GLY* 1.3 72.7 - - - -
76B VAL* 1.3 65.2 + - - +
77B LEU* 3.4 5.6 + - + +
89B ILE* 3.3 5.6 - - - +
90B LYS* 2.8 41.9 + - - +
92B ASP* 4.5 0.7 + - - -
118B VAL* 3.7 27.3 - - + +
161B VAL* 4.1 18.8 - - + -
162B MET* 4.1 21.7 - - - +
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Residues in contact with VAL 76 (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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53B ILE* 3.4 32.3 - - + +
54B VAL* 3.8 9.0 - - - -
55B GLY* 3.0 26.3 + - - -
56B CYS 3.0 14.2 + - - +
58B ILE* 3.9 32.3 - - + -
75B THR* 1.3 71.9 - - - +
77B LEU* 1.3 61.5 + - - +
78B ASP 3.9 9.0 - - - +
87B TYR* 3.8 28.5 - - + -
88B LEU 3.6 5.6 - - - +
89B ILE* 4.5 4.3 - - + +
102B LEU* 4.3 5.4 - - + -
161B VAL* 3.8 2.9 - - - +
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Residues in contact with LEU 77 (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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54B VAL* 3.9 6.0 - - - +
75B THR* 3.8 16.2 - - + +
76B VAL* 1.3 75.5 - - - +
78B ASP* 1.3 61.5 + - - +
88B LEU* 2.6 16.9 + - + +
89B ILE 4.4 0.2 - - - -
90B LYS* 4.1 11.2 - - + +
97B VAL* 4.1 16.2 - - + -
160B PRO* 3.6 31.4 - - + +
161B VAL* 3.5 23.9 - - + +
162B MET* 4.0 25.4 - - + -
167B TYR* 4.1 23.1 - - + +
178B MET* 3.6 29.2 - - + -
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Residues in contact with ASP 78 (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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54B VAL* 4.0 13.8 - - - +
76B VAL* 3.6 3.2 - - - +
77B LEU* 1.3 82.6 - - + +
79B GLN* 1.3 86.6 + - - +
80B VAL* 4.3 0.4 - - - -
81B PRO* 6.1 0.7 - - - -
87B TYR* 3.6 10.9 - - - -
88B LEU* 3.1 43.7 + - + +
160B PRO* 4.6 13.2 - - + +
167B TYR* 5.0 1.5 + - - +
234B HIS* 6.0 1.4 - - - -
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Residues in contact with GLN 79 (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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52B ASN* 3.0 27.1 + - - -
54B VAL* 3.7 13.4 - - + +
78B ASP* 1.3 93.7 + - - +
80B VAL* 1.3 66.6 + - - +
81B PRO* 3.3 8.8 - - - +
84B PRO* 2.4 53.9 + - + +
86B LEU 3.7 7.6 - - - +
87B TYR* 3.8 21.1 + - + -
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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