Contacts of the strand formed by residues 72 - 76 (chain L) in PDB entry 1J0B
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 72 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ALA* 3.6 2.7 - - - +
71L ASP* 1.3 83.5 - - - +
73L VAL* 1.3 73.8 + - - +
74L ILE* 4.4 3.8 - - + -
96L LEU* 4.9 0.8 - - - +
97L ASP* 3.5 27.4 - - + +
99L ILE* 4.2 11.4 - - + -
144L LEU* 3.2 37.9 - - + -
149L ARG* 4.0 13.7 - - - +
150L LYS 3.4 3.0 + - - +
151L PRO* 3.3 22.4 - - + +
152L TYR* 3.2 23.0 + - - +
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62L LEU* 4.5 6.7 - - + -
65L ALA* 5.7 4.5 - - + -
72L VAL* 1.3 75.6 - - - +
74L ILE* 1.3 69.2 + - - +
75L THR* 4.2 1.3 - - + +
87L THR* 3.7 30.1 - - + -
88L GLY* 5.8 0.9 - - - -
91L ALA* 3.3 28.9 - - + -
96L LEU* 4.2 16.4 - - + -
97L ASP 3.3 14.3 + - - +
98L ALA* 3.6 4.9 - - - -
99L ILE* 3.1 32.5 + - - +
152L TYR* 3.8 8.3 - - + +
154L ILE* 4.0 15.0 - - + -
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Residues in contact with ILE 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L VAL* 4.4 3.6 - - + -
73L VAL* 1.3 84.2 - - - +
75L THR* 1.3 59.4 + - - +
99L ILE* 3.5 28.9 - - + -
101L VAL* 4.4 2.2 - - + -
137L ALA* 3.1 38.6 - - + +
140L ILE* 5.0 2.5 - - + -
141L ALA* 3.3 15.9 - - + +
144L LEU* 4.5 2.7 - - + -
151L PRO* 3.3 32.8 - - + -
152L TYR 3.3 5.2 + - - +
153L VAL* 3.1 31.4 - - + +
154L ILE 3.0 22.8 + - - -
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Residues in contact with THR 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L VAL* 5.0 0.4 - - + -
74L ILE* 1.3 75.9 - - - +
76L VAL* 1.3 64.2 + - - +
83L HIS* 2.9 25.1 + - - -
84L ALA* 3.8 21.5 - - + +
87L THR* 3.4 37.0 - - + -
88L GLY 5.0 0.2 - - - +
99L ILE 3.1 13.1 + - - +
100L LEU* 3.3 8.9 - - + +
101L VAL 3.1 19.3 + - - -
154L ILE* 3.6 19.6 + - - +
155L PRO 4.1 0.2 + - - -
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Residues in contact with VAL 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L THR* 1.3 82.1 + - - +
77L GLY* 1.3 62.3 + - - +
81L SER* 4.9 1.6 + - - -
83L HIS* 4.6 6.4 + - - -
84L ALA* 4.7 7.0 - - - +
101L VAL* 3.5 30.7 - - + +
131L PHE* 3.9 14.6 - - + +
133L LEU* 3.8 14.1 - - + +
134L MET* 3.4 32.5 - - + -
137L ALA* 3.8 21.5 - - + -
154L ILE 4.1 3.0 + - - -
156L PRO* 4.2 23.5 - - + +
157L GLY 4.5 4.2 + - - -
1121L 5PA 5.4 0.5 - - - +
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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
------------------------------------------------------------
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