Contacts of the strand formed by residues 146 - 153 (chain C) in PDB entry 5J12
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 4.6 1.8 - - + -
119C PRO* 4.8 2.5 - - + -
141C LEU* 3.8 17.0 - - + -
143C TYR* 3.4 48.7 - - + +
144C GLY 3.4 17.5 - - - +
145C ASP* 1.3 82.5 - - - +
147C LEU* 1.4 65.6 + - - +
148C TYR* 3.8 23.1 - - + +
166C ASN* 3.6 29.6 + - - +
187C VAL* 3.8 11.9 - - + -
188C LYS 3.2 8.5 - - - +
189C ALA* 4.0 13.5 - - + +
190C MET* 4.2 1.2 - - - +
194C TYR* 4.0 8.7 - - + -
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU* 1.4 76.3 - - - +
148C TYR* 1.3 62.6 + - - +
149C GLU 3.5 3.3 + - - -
164C GLN* 3.6 43.1 - - + +
165C GLU* 3.4 15.3 - - - +
166C ASN* 4.4 8.3 - - - +
187C VAL* 3.5 1.7 - - - -
188C LYS* 2.8 49.6 + - + +
189C ALA 5.1 1.1 - - - +
190C MET* 3.8 29.8 - - + -
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Residues in contact with TYR 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C PRO* 5.6 0.2 - - + -
138C CYS* 4.2 0.7 - - - -
139C SER 4.3 4.3 - - - -
140C ASP* 3.5 24.4 + - - +
141C LEU* 2.8 28.7 + - + -
143C TYR 4.6 1.4 + - - -
146C LEU* 3.8 23.7 - - + +
147C LEU* 1.3 71.1 - - - +
149C GLU* 1.3 56.6 + - - +
164C GLN* 3.2 3.5 - - - -
165C GLU 2.7 31.5 + - - +
166C ASN 3.4 22.7 - - - -
167C THR* 3.6 26.9 - - - +
168C CYS* 3.6 31.9 - - + -
170C VAL* 3.6 10.7 - - + +
185C VAL* 5.2 2.7 - - + -
186C ARG 3.6 5.2 - - - +
187C VAL* 3.7 34.1 - - + -
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Residues in contact with GLU 149 (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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147C LEU 3.5 0.8 + - - -
148C TYR* 1.3 71.7 - - - +
150C VAL* 1.3 65.4 + - - +
151C GLN* 3.1 26.8 + - - +
162C SER* 2.7 30.7 + - - +
163C LYS 3.7 4.5 - - - +
164C GLN* 3.7 16.2 - - + +
185C VAL* 3.3 4.3 - - - -
186C ARG* 2.8 66.2 + - + +
188C LYS* 3.0 26.2 + - - -
203C TRP* 3.9 7.5 - - + -
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Residues in contact with VAL 150 (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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136C VAL* 4.1 20.6 - - + +
148C TYR 5.0 0.2 - - - +
149C GLU* 1.3 75.6 - - - +
151C GLN* 1.3 63.9 + - - +
152C TYR* 4.1 2.4 - - - -
162C SER* 3.4 3.3 + - - -
163C LYS 2.8 35.3 + - - +
168C CYS* 6.3 0.7 - - - -
170C VAL* 3.8 33.9 - - + -
172C ILE* 3.8 20.4 - - + -
183C PHE* 3.9 22.4 - - + -
184C TRP 3.5 7.4 - - - +
185C VAL* 4.2 19.1 - - + +
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Residues in contact with GLN 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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149C GLU* 3.1 27.9 + - - +
150C VAL* 1.3 74.0 - - - +
152C TYR* 1.3 62.7 + - - +
160C TRP* 3.3 32.2 + - + +
161C GLN 3.2 13.0 - - - +
162C SER* 3.8 6.9 - - - -
183C PHE* 3.4 6.1 - - - -
184C TRP* 2.9 59.6 + - + +
186C ARG* 4.6 4.4 - - - +
203C TRP* 3.4 23.2 - - + -
301C SO4 4.8 7.1 + - - -
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Residues in contact with TYR 152 (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 VAL 4.1 2.7 - - - -
151C GLN* 1.3 77.7 - - - +
153C ARG* 1.3 64.1 + - - +
157C ASP* 5.5 2.5 - - - -
160C TRP* 3.5 5.5 - - - -
161C GLN* 2.9 68.1 + - + +
162C SER* 4.0 12.0 + - - -
163C LYS* 4.8 1.8 - - + +
172C ILE* 3.7 42.8 - - + +
175C LEU* 3.8 26.4 - - + +
181C TYR* 4.3 13.0 - + + -
182C SER 3.1 13.5 - - - +
183C PHE* 3.5 22.7 - + + -
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Residues in contact with ARG 153 (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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152C TYR* 1.3 78.1 - - - +
154C SER* 1.3 65.4 + - - +
157C ASP* 3.3 22.2 + - + -
158C THR* 3.1 32.1 + - - +
159C GLU* 3.9 18.4 - - - +
160C TRP* 3.3 59.9 - - + +
181C TYR* 3.3 9.1 - - - -
182C SER* 2.8 37.3 + - - +
218C CYS* 5.2 0.2 - - - -
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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