Contacts of the strand formed by residues 73 - 77 (chain B) in PDB entry 3H8E
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 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.3 21.3 - - + +
20B ILE* 4.1 15.5 - - + -
43B ILE* 4.4 6.1 - - + -
60B LEU 3.8 1.6 - - - +
61B LEU* 3.6 2.4 - - - -
62B LEU* 2.7 48.5 + - + +
63B GLN 4.6 1.0 + - - +
65B LEU* 4.2 9.9 - - + +
68B LEU* 3.5 30.7 - - + -
70B ALA* 4.6 5.2 - - + +
72B ARG* 1.3 77.3 - - - +
74B LEU* 1.3 62.2 + - - +
75B LEU* 3.8 26.2 + - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B THR* 4.0 17.0 - - + +
18B LEU 2.8 10.2 + - - +
19B VAL* 3.2 14.0 - - + +
20B ILE* 3.0 26.9 + - - +
59B THR* 3.8 27.6 - - + -
60B LEU 3.7 13.2 - - - +
61B LEU* 4.0 10.8 - - + -
73B VAL* 1.3 73.3 - - - +
75B LEU* 1.3 64.6 + - - +
76B VAL* 5.3 0.2 - - + -
96B VAL* 4.0 32.3 - - + +
99B VAL* 4.0 37.2 - - + -
100B LEU* 4.3 5.8 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.4 35.0 - - + -
22B VAL* 3.9 9.9 - - + -
43B ILE* 4.0 22.7 - - + +
46B VAL* 5.5 1.8 - - + -
47B LEU* 3.9 27.8 - - + -
52B LEU* 3.7 13.8 - - + +
59B THR* 3.2 9.0 - - - +
60B LEU* 2.9 51.6 + - + +
62B LEU* 4.4 16.6 - - + -
73B VAL* 3.8 11.9 - - + +
74B LEU* 1.3 71.5 - - - +
76B VAL* 1.3 60.1 + - - +
77B GLY 4.3 0.2 - - - -
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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
----------------------------------------------------------
19B VAL* 4.0 5.8 - - + -
20B ILE 2.9 18.6 + - - +
21B PRO* 3.1 4.7 - - + +
22B VAL* 2.9 24.5 + - - +
52B LEU* 4.9 0.4 - - - -
57B GLY* 3.8 5.8 - - - -
58B GLN 3.3 10.3 - - - +
59B THR* 4.1 7.0 - - + -
74B LEU* 5.3 0.2 - - + -
75B LEU* 1.3 77.2 - - - +
77B GLY* 1.3 65.5 + - - +
92B LEU* 2.8 40.6 - - + +
95B SER* 5.3 0.2 - - - -
96B VAL* 3.7 27.4 - - + -
112B LEU* 4.0 22.0 - - + -
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Residues in contact with GLY 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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22B VAL 3.2 9.0 - - - -
52B LEU* 4.7 3.9 - - - +
54B GLY* 3.6 12.3 - - - -
55B LYS 3.3 19.1 - - - -
56B PRO* 3.3 0.7 - - - +
57B GLY 2.9 19.8 + - - -
58B GLN 2.8 15.0 + - - -
76B VAL* 1.3 72.8 - - - +
78B SER* 1.4 59.2 + - - -
79B GLY 3.6 2.0 - - - -
92B LEU* 3.4 11.1 - - - +
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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