Contacts of the strand formed by residues 180 - 189 (chain C) in PDB entry 1JZ3
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 180 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C ASN* 3.2 19.8 - - - -
129C VAL 2.9 24.6 + - - -
179C ALA* 1.3 73.0 - - - +
181C GLU* 1.3 61.0 + - - -
182C ASN* 2.8 17.0 + - - -
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Residues in contact with GLU 181 (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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126C THR* 3.4 23.3 - - + +
127C PHE* 3.1 22.9 + - - +
128C ASN* 3.6 17.4 - - - +
155C ASN* 4.6 0.5 - - - +
178C ARG* 3.9 18.4 + - - +
179C ALA 4.0 1.0 + - - -
180C GLY* 1.3 73.0 - - - -
182C ASN* 1.3 64.4 + - - +
3006C MG 4.2 3.3 - - - -
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Residues in contact with ASN 182 (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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126C THR* 3.1 6.5 - - - +
127C PHE* 2.7 52.6 + - + +
129C VAL* 3.7 15.2 - - - +
154C CYS* 5.1 0.2 - - - -
155C ASN* 2.8 31.3 + - - +
177C LEU* 3.3 13.9 - - + -
178C ARG* 2.9 33.7 + - - +
180C GLY 2.8 27.7 + - - -
181C GLU* 1.3 75.9 - - - +
183C ARG* 1.4 62.3 + - - +
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Residues in contact with ARG 183 (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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73C TRP* 2.7 43.4 + - - +
74C LEU* 3.1 21.2 + - - +
75C GLU 3.8 6.4 - - - -
76C CYS* 3.4 22.8 + - - +
77C ASP* 3.7 18.3 + - - +
124C SER* 3.4 29.3 + - - -
125C LEU 3.3 8.1 - - - +
126C THR* 4.0 17.7 - - + +
127C PHE* 4.5 0.4 - - - -
153C TRP 4.8 0.2 - - - -
154C CYS* 3.5 1.7 - - - -
155C ASN* 2.7 43.1 + - - +
156C GLY 4.6 0.5 + - - -
182C ASN* 1.4 77.1 - - - +
184C LEU* 1.3 70.2 + - - +
185C ALA* 4.4 6.4 - - - +
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Residues in contact with LEU 184 (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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54C LEU* 4.2 11.9 - - + -
58C TRP* 4.0 22.0 - - + -
124C SER* 3.1 25.4 - - - -
125C LEU* 3.0 17.7 + - + +
127C PHE* 3.5 27.6 - - + -
141C ILE* 3.2 35.0 - - + -
143C PHE* 4.6 4.5 - - + -
152C LEU* 4.5 5.6 - - + -
153C TRP 3.5 8.1 - - - +
154C CYS* 4.1 17.9 - - + -
173C LEU* 4.2 5.8 - - + -
183C ARG* 1.3 78.7 - - - +
185C ALA* 1.3 61.3 + - - +
186C VAL* 4.6 7.9 - - + -
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Residues in contact with ALA 185 (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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73C TRP* 3.6 30.1 - - + -
74C LEU* 4.4 7.4 - - + +
123C TYR 3.4 4.3 - - - -
124C SER* 4.2 0.9 - - - -
152C LEU* 3.5 1.9 - - - -
153C TRP* 2.8 51.8 + - + +
183C ARG* 4.4 14.6 - - - +
184C LEU* 1.3 76.0 - - - +
186C VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 186 (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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58C TRP* 4.3 13.5 - - + -
73C TRP* 3.6 2.7 - - - -
121C GLY 3.3 3.8 - - - +
122C CYS* 3.6 1.4 - - - -
123C TYR* 2.7 44.5 + - + +
143C PHE* 3.8 28.0 - - + -
146C VAL* 5.2 0.4 - - + -
150C PHE* 3.6 32.3 - - + -
151C HIS 3.4 2.7 - - - +
152C LEU* 3.8 8.5 - - + -
184C LEU* 4.6 3.1 - - + -
185C ALA* 1.3 82.5 - - - +
187C MET* 1.3 59.4 + - - +
188C VAL* 3.7 17.0 + - + -
208C ILE* 4.0 15.3 - - + -
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Residues in contact with MET 187 (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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16C TRP* 5.0 5.6 - - + -
66C PRO* 4.1 18.6 - - + +
69C VAL* 4.4 13.7 - - - -
73C TRP* 3.8 9.3 - - + -
120C THR* 3.4 29.8 - - + -
121C GLY 3.7 1.8 - - - -
122C CYS* 4.5 7.2 - - - +
150C PHE* 3.2 4.7 - - - -
151C HIS* 3.0 56.5 + - + -
153C TRP* 3.6 27.1 - - + -
186C VAL* 1.3 71.7 - - - +
188C VAL* 1.3 59.8 + - - +
189C LEU* 3.9 16.1 + - + +
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Residues in contact with VAL 188 (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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90C TRP* 3.5 16.9 - - + -
120C THR* 3.3 5.9 - - - -
121C GLY 2.7 39.4 + - - +
123C TYR* 3.7 27.4 - - + -
146C VAL* 3.8 26.0 - - + -
147C ASN 3.5 24.5 - - - +
149C ALA 3.5 9.9 - - - +
150C PHE* 4.2 0.4 - - + -
186C VAL* 3.9 14.6 - - + -
187C MET* 1.3 77.0 - - - +
189C LEU* 1.4 64.7 + - - +
207C GLY* 4.3 4.3 - - - +
208C ILE* 4.0 2.9 - - + -
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Residues in contact with LEU 189 (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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16C TRP* 3.0 57.9 - - + -
66C PRO* 4.0 22.7 - - + -
118C ASN* 4.1 6.1 - - - +
119C PRO 4.0 1.8 - - - -
120C THR* 3.9 21.8 - - + +
148C SER* 2.9 27.4 + - - -
149C ALA* 2.9 25.5 + - + +
150C PHE* 5.3 0.4 - - - +
151C HIS* 5.6 0.2 - - + -
161C TYR* 4.9 3.8 - - + +
187C MET* 4.4 14.6 - - + +
188C VAL* 1.4 74.5 - - - +
190C ARG* 1.3 62.0 + - - +
191C TRP 3.6 13.5 - - - +
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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