Contacts of the strand formed by residues 68 - 71 (chain B) in PDB entry 2J16
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 ILE 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 3.9 0.7 - - - +
63B VAL* 2.9 26.6 + - + +
64B LEU* 3.4 24.2 + - + -
66B GLU* 3.4 17.9 - - + +
67B LYS* 1.3 76.2 - - - +
69B TYR* 1.3 67.4 + - - +
126B ILE* 3.6 16.6 - - + -
130B THR* 4.3 1.6 - - + -
136B ILE* 3.6 25.4 - - + +
138B ILE* 4.0 26.5 - - + -
151B ILE* 4.3 15.7 - - + -
154B TYR* 3.6 33.4 - - + -
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.6 1.4 - - - +
165A HIS* 4.9 12.6 + + - -
60B PRO* 3.8 14.6 - - + -
61B LEU 3.1 7.6 - - - +
62B LEU* 3.6 44.5 - - + +
63B VAL* 4.8 0.7 - - - -
67B LYS* 3.6 23.2 - - + +
68B ILE* 1.3 80.8 - - - +
70B LEU* 1.3 60.5 + - - +
82B PHE* 3.5 30.3 - + + -
135B LYS* 3.7 36.7 + - + -
136B ILE 2.9 11.7 + - - +
137B LEU* 3.9 10.5 - - + -
138B ILE* 3.0 31.7 + - - +
151B ILE* 4.2 0.4 - - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.4 29.6 - - + +
60B PRO* 3.7 0.3 - - - +
61B LEU* 2.9 33.2 + - + +
63B VAL* 4.0 16.4 - - + -
69B TYR* 1.3 76.7 - - - +
71B TYR* 1.3 70.9 + - - +
137B LEU* 4.2 0.7 - - - -
138B ILE 3.3 2.5 - - - +
143B GLY 4.8 4.5 - - - +
147B SER* 3.5 39.7 - - - +
148B ALA* 4.3 2.2 - - - +
151B ILE* 4.1 13.5 - - + -
170B LEU* 4.6 8.3 - - + -
174B ALA* 4.0 22.4 - - + -
177B ILE* 4.0 11.9 - - + -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.6 36.7 + - + -
57B PRO 5.4 0.3 + - - -
59B GLY* 3.4 28.0 - - - -
60B PRO* 3.5 26.9 - - + -
70B LEU* 1.3 75.2 - - - +
72B SER* 1.3 89.1 + - - +
73B GLU 4.4 4.0 - - - -
74B PRO* 4.0 16.2 - - + -
78B GLU* 2.8 43.0 + - - -
137B LEU* 3.8 16.2 - - + -
138B ILE 3.1 6.7 + - - -
139B HIS* 3.3 19.9 - - + -
140B CYS 3.6 3.3 + - - -
143B GLY* 4.1 6.7 - - - -
147B SER* 4.1 2.9 + - - -
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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