Contacts of the strand formed by residues 78 - 83 (chain B) in PDB entry 3SN6
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 LYS 78 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 4.6 13.5 - - - +
30A LEU* 4.2 22.3 - - + +
33A ASP* 3.6 38.0 + - - -
53B GLY 5.8 0.4 - - - +
54B HIS* 4.0 6.2 - - - +
55B LEU* 5.2 4.3 - - + -
73B ALA* 3.9 1.4 - - - +
74B SER 3.2 24.8 + - - +
76B ASP* 2.8 25.2 + - + +
77B GLY* 1.3 81.8 - - - +
79B LEU* 1.3 60.2 + - - +
80B ILE* 4.1 13.9 - - + -
92B ALA* 4.9 13.4 + - + +
93B ILE 3.8 6.5 - - - +
94B PRO* 4.0 34.8 - - + +
95B LEU* 4.6 2.0 - - - +
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Residues in contact with LEU 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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71B VAL* 3.6 17.0 - - + -
72B SER 3.1 32.5 - - - +
73B ALA* 3.5 16.4 - - + -
78B LYS* 1.3 75.1 - - - +
80B ILE* 1.3 62.3 + - - +
81B ILE* 5.6 1.3 - - + -
91B HIS 3.9 0.5 - - - +
92B ALA* 3.6 1.6 - - - -
93B ILE* 2.9 63.6 + - + +
95B LEU* 4.2 8.5 - - + -
103B CYS* 4.0 5.4 - - + -
112B VAL* 3.5 27.1 - - + -
114B CYS* 4.3 15.0 - - + -
124B TYR* 4.1 15.0 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.3 6.3 - - + -
53B GLY* 3.4 40.8 - - - +
54B HIS* 3.7 21.1 - - + +
71B VAL* 3.6 0.6 - - - -
72B SER 2.9 37.1 + - - -
78B LYS* 4.1 10.7 - - + -
79B LEU* 1.3 75.5 - - - +
81B ILE* 1.3 65.5 + - - +
82B TRP* 3.1 36.1 - - + +
89B LYS* 3.7 23.3 - - + -
91B HIS 3.4 10.8 - - - +
92B ALA* 4.8 8.5 - - + -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.5 4.7 - - + -
70B LEU 3.4 6.3 - - - +
71B VAL* 3.7 15.3 - - + -
79B LEU* 5.1 0.9 - - + +
80B ILE* 1.3 73.6 - - - +
82B TRP* 1.3 60.9 + - - +
89B LYS* 3.7 1.2 - - - -
90B VAL* 2.8 49.4 + - + -
91B HIS* 2.9 32.5 + - + +
93B ILE* 4.7 8.5 - - + -
105B TYR* 3.8 17.3 - - + +
112B VAL* 3.9 13.0 - - + -
126B LEU* 3.3 44.9 - - + -
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Residues in contact with TRP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.3 58.1 - - + -
52B ARG 3.3 4.0 - - - -
53B GLY* 2.7 37.2 - - - -
54B HIS* 3.8 18.8 - + - -
69B LEU* 3.0 15.0 - - - +
70B LEU* 2.9 49.0 + - + +
72B SER* 2.8 22.8 + - - -
80B ILE* 3.1 33.6 - - + +
81B ILE* 1.3 74.4 - - - +
83B ASP* 1.3 63.2 + - - +
87B THR* 4.8 3.8 - - - -
88B ASN 3.4 12.6 - - - +
89B LYS* 3.5 23.6 - - + +
90B VAL* 4.4 1.3 - - - -
336B LEU* 3.8 4.5 - - + +
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Residues in contact with ASP 83 (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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19A GLN* 3.2 25.5 + - - +
68B ARG* 2.7 48.6 + - - +
69B LEU* 3.8 12.4 - - + +
82B TRP* 1.3 77.5 - - - +
84B SER* 1.3 57.3 + - - +
85B TYR 3.2 8.8 + - - -
86B THR* 3.3 18.8 + - - +
87B THR* 2.7 36.4 + - - -
88B ASN* 3.2 9.0 + - + +
90B VAL* 4.1 3.6 - - + -
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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