Contacts of the strand formed by residues 146 - 151 (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 LEU 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 3.6 15.2 - - - +
102B THR* 3.4 15.4 - - + +
114B CYS 3.9 0.7 - - - +
115B GLY* 3.6 18.4 - - - +
116B GLY 3.0 22.8 + - - +
119B ASN* 4.4 1.1 - - - +
120B ILE 3.9 6.7 - - - +
121B CYS* 3.4 41.3 - - + +
142B HIS* 3.5 33.0 - - + -
144B GLY 3.7 0.6 + - - -
145B TYR* 1.3 72.4 - - - +
147B SER* 1.3 62.4 + - - +
148B CYS 4.1 6.1 - - - +
149B CYS* 4.7 1.1 - - - -
159B THR* 3.5 16.6 - - + +
160B SER 3.4 15.5 - - - +
161B SER* 4.1 0.7 - - - -
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Residues in contact with SER 147 (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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101B MET* 3.4 11.7 - - - +
102B THR* 3.1 15.8 + - - -
145B TYR* 3.5 24.8 + - - -
146B LEU* 1.3 73.2 - - - +
148B CYS* 1.3 59.4 + - - +
160B SER* 2.8 27.4 + - - -
161B SER* 4.5 0.4 - - - -
187B VAL 2.3 30.6 + - - -
188B MET* 3.4 21.2 + - - +
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Residues in contact with CYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 3.5 12.1 - - - +
146B LEU* 3.6 3.0 - - - +
147B SER* 1.3 83.4 + - - +
149B CYS* 1.3 79.9 + - - +
150B ARG* 4.9 10.3 - - - -
159B THR* 3.3 2.1 - - - -
160B SER* 2.7 43.0 + - - +
188B MET 4.0 0.2 - - - +
189B SER* 3.8 17.7 - - - +
190B LEU* 3.4 38.4 - - - -
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Residues in contact with CYS 149 (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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102B THR* 4.0 15.7 + - - -
103B CYS* 4.6 2.0 - - - +
104B ALA* 3.1 29.8 - - - +
113B ALA* 4.3 10.8 - - - -
114B CYS 5.1 0.4 - - - -
121B CYS* 4.1 18.8 - - - -
146B LEU* 4.7 1.8 - - + -
148B CYS* 1.3 85.4 - - - +
150B ARG* 1.3 82.1 + - - +
157B ILE* 4.4 2.5 - - + -
158B VAL 3.0 17.7 - - - +
159B THR* 3.4 16.8 - - + +
190B LEU* 4.2 2.7 - - - -
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Residues in contact with ARG 150 (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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61B MET 4.7 5.9 + - - -
62B HIS* 3.6 47.4 + - - +
102B THR* 5.2 1.2 + - - -
103B CYS 3.4 20.8 + - - -
104B ALA* 3.7 4.2 - - - +
148B CYS* 4.9 10.9 - - - -
149B CYS* 1.3 96.7 + - - +
151B PHE* 1.3 61.5 + - - +
157B ILE* 3.1 7.3 - - - +
158B VAL* 2.7 40.6 + - + +
190B LEU* 3.5 25.0 + - + +
191B SER* 5.5 1.0 - - - +
192B LEU* 3.5 29.8 - - + +
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Residues in contact with PHE 151 (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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62B HIS* 6.0 0.6 - - - -
104B ALA* 3.9 7.1 - - + +
105B TYR 3.6 7.4 + - - +
106B ALA* 3.2 34.3 - - + -
107B PRO* 3.6 23.7 - - + +
111B TYR* 4.0 22.7 - - + -
113B ALA* 3.7 26.9 - - + -
123B ILE* 3.6 23.3 - - + -
150B ARG* 1.3 73.7 - - - +
152B LEU* 1.3 62.9 + - - +
153B ASP 3.2 18.8 - - - +
154B ASP* 4.8 1.8 - - - -
156B GLN 4.4 0.2 - - - -
157B ILE* 3.9 12.6 - - + -
171B ILE* 3.5 25.8 - - + -
192B LEU* 3.7 11.6 - - - +
196B THR* 5.3 0.9 - - - +
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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