Contacts of the strand formed by residues 150 - 155 (chain C) in PDB entry 3J82
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 GLY 150 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG* 6.0 0.2 - - - -
149C THR* 1.3 77.3 - - - +
151C ILE* 1.3 57.6 + - - -
152C VAL* 4.1 1.3 + - - -
163C VAL 4.0 0.7 - - - +
164C PRO* 3.5 0.7 - - - +
165C ILE* 2.7 36.1 + - - +
292C ASP* 4.5 1.0 + - - -
293C LEU* 4.4 12.0 - - - +
296C ASN* 2.8 22.9 - - - -
298C VAL* 5.6 3.1 - - - -
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Residues in contact with ILE 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLY* 1.3 73.1 - - - +
152C VAL* 1.3 67.6 + - - +
153C MET 4.1 0.2 + - - -
162C THR* 4.6 5.2 - - - -
163C VAL 3.7 10.8 - - - +
164C PRO* 3.9 6.1 - - + -
278C THR* 3.6 42.0 - - + +
281C SER* 3.7 20.2 - - - +
282C ILE* 4.5 7.4 - - + +
293C LEU* 3.4 41.8 + - + +
294C TYR* 5.1 0.7 - - - -
296C ASN 2.6 9.6 + - - +
297C THR* 3.1 31.9 - - + -
298C VAL* 3.2 1.5 + - - +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LEU* 4.9 13.7 - - + -
150C GLY 4.1 1.5 - - - -
151C ILE* 1.3 76.8 - - - +
153C MET* 1.3 65.6 + - - +
154C ASP* 4.6 6.3 - - + +
161C HIS 3.7 0.2 - - - +
162C THR* 3.3 23.8 - - - -
163C VAL* 3.1 33.5 + - + +
165C ILE* 5.7 0.7 - - + -
278C THR* 5.9 0.7 - - - -
298C VAL* 2.8 34.5 - - + +
300C SER* 3.3 26.5 - - - +
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Residues in contact with MET 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ILE 4.1 0.2 + - - -
152C VAL* 1.3 75.1 - - - +
154C ASP* 1.3 53.7 + - - +
155C SER* 4.7 3.6 - - - +
160C THR* 6.2 0.2 - - + -
161C HIS 3.6 5.6 - - - +
162C THR* 4.5 4.9 - - + -
274C ILE* 4.1 35.0 - - + -
278C THR* 5.3 3.3 - - + +
297C THR* 6.0 2.7 - - - +
298C VAL 2.6 13.2 + - - +
299C LEU* 2.8 52.9 - - + +
300C SER 2.6 32.7 + - - -
304C THR* 4.1 10.5 - - + -
309C ILE* 5.6 2.9 - - + -
313C MET* 3.2 35.7 - - + +
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Residues in contact with ASP 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ALA* 4.9 11.6 - - + +
141C SER* 4.3 14.5 + - - -
152C VAL* 3.7 7.8 + - + +
153C MET* 1.3 72.1 - - - +
155C SER* 1.3 66.5 + - - +
156C GLY 5.1 1.3 - - - -
159C VAL 4.8 1.3 - - - +
160C THR* 3.2 4.0 - - - +
161C HIS* 2.8 47.0 + - + +
300C SER* 2.7 38.2 - - - +
301C GLY* 3.2 6.9 + - - -
339C VAL* 5.0 7.0 - - - +
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C MET* 4.7 4.6 - - - +
154C ASP* 1.3 75.4 + - - +
156C GLY* 1.3 59.7 + - - +
159C VAL 4.1 0.4 - - - -
160C THR* 2.6 30.0 + - - +
261C LEU* 5.2 0.7 - - - +
274C ILE* 4.2 14.2 - - - +
300C SER 2.6 11.4 + - - +
301C GLY* 3.0 13.7 - - - -
303C THR* 2.9 41.6 + - - +
304C THR* 3.7 11.6 + - - +
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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
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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