Contacts of the strand formed by residues 155 - 160 (chain C) in PDB entry 2Z9I
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 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C SER* 3.9 22.0 - - - +
88C ASP* 4.6 4.0 - - + +
140C ARG 3.0 4.0 - - - +
141C PRO* 3.2 4.9 - - - +
142C VAL* 2.7 57.7 + - + +
144C THR* 4.3 5.6 - - + -
153C THR* 3.3 24.7 - - - +
154C VAL* 1.3 76.9 - - - +
156C ASP* 1.3 59.7 + - - +
157C ALA* 3.4 13.5 - - + +
185C SER* 4.0 25.6 - - - -
186C ALA* 4.7 8.3 - - + -
206C PHE* 5.0 3.4 - - + -
208C ILE* 4.0 20.2 - - + +
212C GLN* 5.8 0.2 - - - -
282C ALA* 3.8 2.9 - - - +
410F GLN* 6.0 2.0 - - - +
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Residues in contact with ASP 156 (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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139C ASN* 3.2 43.4 + - - +
140C ARG 3.6 3.8 - - - -
154C VAL 4.1 0.8 + - - -
155C LEU* 1.3 70.6 - - - +
157C ALA* 1.3 61.0 + - - +
209C PRO* 3.2 27.3 - - - +
212C GLN* 3.1 24.6 + - - +
282C ALA* 3.6 31.1 - - + +
283C ALA* 4.7 2.5 + - - -
285C ARG* 5.4 1.1 - - + +
286C SER* 3.0 29.0 + - - +
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Residues in contact with ALA 157 (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 LEU 3.7 0.5 - - - -
139C ASN 2.9 11.4 + - - -
140C ARG* 2.7 39.7 + - - +
142C VAL* 4.2 5.2 - - + -
155C LEU* 4.3 10.8 - - + -
156C ASP* 1.3 75.3 - - - +
158C ILE* 1.3 64.1 + - - +
159C GLN 3.8 0.2 + - - -
206C PHE* 3.8 32.1 - - + -
207C ALA 3.2 15.3 - - - +
209C PRO* 4.3 0.7 - - - -
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Residues in contact with ILE 158 (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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108C SER* 4.7 0.7 - - - -
111C LEU* 3.4 30.3 - - + -
135C VAL* 4.2 9.6 - - + -
137C ALA 3.8 3.8 - - - +
138C LEU* 4.1 16.8 - - + -
139C ASN 5.9 0.2 - - - +
157C ALA* 1.3 74.0 - - - +
159C GLN* 1.3 71.0 + - - +
160C THR* 4.1 0.9 + - - +
173C LEU* 4.1 17.0 - - + -
181C VAL 3.3 26.2 - - - +
182C GLY* 4.1 9.2 - - - -
205C GLY 3.7 0.2 - - - +
206C PHE* 3.3 4.0 - - - -
207C ALA* 2.8 39.3 + - + +
209C PRO* 3.6 28.9 - - + -
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Residues in contact with GLN 159 (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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126A LEU* 4.0 8.1 - - - +
129A THR* 2.9 33.0 + - - +
135C VAL* 3.6 4.3 - - - -
136C SER* 2.7 31.7 + - - -
137C ALA* 2.8 25.9 + - + +
140C ARG* 2.8 46.2 - - + +
157C ALA 3.8 1.8 + - - -
158C ILE* 1.3 75.3 - - - +
160C THR* 1.3 62.2 + - - +
204C LEU* 3.6 12.0 - - - +
205C GLY 3.2 12.6 - - - +
206C PHE* 3.5 27.1 - - + -
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Residues in contact with THR 160 (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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117C VAL* 3.4 17.8 - - - +
134C ILE 2.8 20.2 + - - -
135C VAL* 4.9 0.7 - - - -
136C SER* 3.8 5.6 - - - -
158C ILE* 5.1 2.0 - - - +
159C GLN* 1.3 77.4 - - - +
161C ASP* 1.3 59.1 + - - +
162C ALA* 3.1 12.7 + - - +
164C ILE* 3.3 32.3 - - + -
173C LEU* 4.2 20.6 - - + -
184C ASN* 4.7 0.7 - - - +
203C GLY 3.4 6.7 - - - +
205C GLY* 2.8 41.1 + - - +
206C PHE* 4.8 1.1 - - - +
207C ALA 5.6 0.4 - - - +
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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