Contacts of the strand formed by residues 65 - 73 (chain U) in PDB entry 3J7Y
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 65 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U ARG* 2.7 45.1 + - + +
57U LEU* 3.5 40.6 - - + -
58U GLU* 3.3 10.8 + - + +
63U VAL* 4.0 10.8 - - + +
64U PRO* 1.3 71.9 - - - +
66U ALA* 1.3 56.6 + - - +
67U ALA 3.6 6.7 - - - +
68U VAL* 3.4 32.3 - - + -
97U VAL* 3.6 14.6 - - + -
98U GLN 3.8 3.1 - - - -
99U LEU* 4.8 0.9 - - + +
315s ASN* 3.4 13.8 + - - +
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Residues in contact with ALA 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U ARG* 2.8 17.2 + - - +
64U PRO 3.7 1.6 + - - -
65U VAL* 1.3 72.5 - - - +
67U ALA* 1.3 60.5 + - - +
98U GLN 2.7 16.2 + - - +
99U LEU 3.8 4.5 - - - +
100U ALA* 3.7 26.7 - - + -
100s LEU* 3.2 25.2 - - + +
314s GLN* 3.3 9.2 - - - +
316s CYS* 3.7 21.0 - - + +
319s GLN* 5.4 1.3 - - - +
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Residues in contact with ALA 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U ARG* 3.5 9.4 - - - +
65U VAL* 3.6 2.1 - - - +
66U ALA* 1.3 82.9 - - - +
68U VAL* 1.3 66.1 + - - +
69U ARG* 4.7 9.2 - - - +
96U TYR 4.5 0.7 - - - -
97U VAL* 3.3 3.5 - - - -
98U GLN* 2.8 52.2 + - + +
100s LEU* 4.2 10.5 - - + -
314s GLN* 5.2 0.9 - - - +
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Residues in contact with VAL 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50U ARG* 3.0 52.2 + - + +
53U LEU* 3.5 26.0 - - + -
54U ARG* 3.3 38.9 - - + +
57U LEU* 5.6 0.2 - - + -
65U VAL* 3.4 16.6 - - + -
67U ALA* 1.3 74.2 - - - +
69U ARG* 1.3 73.2 + - - +
70U THR* 4.2 6.1 - - + -
95U ALA* 4.7 0.4 - - + -
96U TYR 3.6 3.4 - - - -
97U VAL* 4.1 10.5 - - + -
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Residues in contact with ARG 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2372A U 3.4 42.1 + - - +
2373A A 3.5 39.5 - - - +
39U THR* 4.9 4.2 - - - +
50U ARG* 3.9 2.0 - - - +
67U ALA* 4.7 8.1 - - + +
68U VAL* 1.3 79.9 - - - +
70U THR* 1.3 62.9 + - - +
95U ALA* 4.3 0.4 - - - -
96U TYR* 2.8 57.9 + - - +
98U GLN* 3.0 43.8 + - - +
98s PHE* 5.2 4.0 - - - -
270s LYS 4.6 4.0 + - - -
272s PRO* 3.3 28.3 - - - +
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Residues in contact with THR 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2372A U 3.7 3.8 - - - +
2373A A 2.9 19.4 + - - -
2419A C 3.6 6.8 + - - -
2420A U 4.1 5.9 + - - -
2422A U 5.4 0.2 - - - +
44U ILE* 5.0 5.2 - - + -
48U MET 5.2 0.7 - - - +
49U THR 4.8 1.8 - - - -
50U ARG* 3.0 47.8 + - - +
53U LEU* 4.9 3.4 - - + -
68U VAL* 4.2 7.9 - - + -
69U ARG* 1.3 73.4 - - - +
71U ARG* 1.3 66.4 + - - +
93U LYS* 3.7 27.1 - - + -
94U VAL 3.3 7.6 - - - +
95U ALA* 4.5 10.3 - - + -
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Residues in contact with ARG 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2370A A 3.8 38.4 + - - +
2371A U 3.4 40.8 + - - +
2372A U 3.5 34.1 - - - +
2420A U 6.0 0.4 - - - -
2422A U 5.8 2.5 - - + -
70U THR* 1.3 79.9 - - - +
72U VAL* 1.3 70.2 + - - +
73U GLN* 3.0 35.2 + - - +
93U LYS* 4.2 3.0 - - - +
94U VAL* 2.8 47.6 + - - +
96U TYR* 2.6 39.3 + - + -
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Residues in contact with VAL 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249 LYS* 3.4 16.9 + - + +
369 ARG* 4.3 7.9 - - + +
2371A U 4.2 8.0 + - - +
2420A U 3.5 27.4 - - - +
2421A G 3.1 37.1 + - - +
2422A U 6.2 0.6 - - - -
46U MET* 3.4 33.4 - - + -
71U ARG* 1.3 84.9 + - - +
73U GLN* 1.3 66.3 + - - +
91U ASP* 4.9 1.6 - - + -
92U TYR 3.8 3.6 - - - +
93U LYS* 4.2 15.3 - - + +
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Residues in contact with GLN 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2370A A 2.5 47.6 + - + +
2371A U 6.5 0.9 - - - -
71U ARG* 3.0 28.5 + - - +
72U VAL* 1.3 77.2 - - - +
74U HIS* 1.3 69.4 - - - +
75U GLY* 5.9 0.6 - - - -
91U ASP* 3.3 3.8 - - - +
92U TYR* 2.7 84.5 + - + +
94U VAL* 3.7 13.3 - - + +
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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