Contacts of the strand formed by residues 179 - 187 (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 GLN 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C SER* 3.3 18.4 - - - -
105C LEU 4.1 11.3 + - - -
106C GLY* 3.7 20.5 - - - +
174C VAL* 3.1 5.8 - - - -
175C ASN* 3.0 52.6 + - - +
177C ASN* 3.6 24.4 + - - +
178C ALA* 1.3 79.7 - - - +
180C LEU* 1.3 64.2 + - - +
181C VAL* 3.4 0.9 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.8 21.5 - - + -
38C LEU* 5.4 0.2 - - + -
45C LEU* 4.0 14.8 - - + -
103C ILE* 4.1 19.8 - - + +
104C SER 2.7 17.2 + - - +
105C LEU* 3.7 26.0 - - + -
106C GLY* 2.8 29.3 + - - -
172C ALA* 3.5 28.9 - - + -
173C LEU 3.7 4.0 - - - +
174C VAL* 4.2 3.6 - - - +
178C ALA 4.2 0.4 + - - -
179C GLN* 1.3 68.8 - - - +
181C VAL* 1.3 58.5 - - - +
182C GLY 3.5 24.7 - - - +
183C VAL* 4.6 4.7 - - + -
210C VAL* 3.6 15.2 - - + +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLY* 4.9 2.5 - - - -
107C SER 4.5 10.8 - - - +
108C SER* 3.7 3.3 - - - -
111C LEU* 4.1 32.8 - - + -
117C VAL* 4.4 4.9 - - + -
158C ILE* 3.3 12.7 - - - +
173C LEU* 2.8 36.0 + - + +
174C VAL 4.1 1.6 - - - -
175C ASN* 3.6 39.3 - - + +
179C GLN 3.6 4.3 - - - +
180C LEU* 1.3 79.1 - - - +
182C GLY* 1.3 60.2 + - - +
210C VAL* 2.9 28.4 + - + +
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Residues in contact with GLY 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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158C ILE* 4.1 9.4 - - - -
172C ALA 3.9 0.2 - - - -
173C LEU* 2.9 37.7 + - - +
180C LEU* 3.5 10.8 - - - +
181C VAL* 1.3 82.0 - - - +
183C VAL* 1.3 63.2 + - - -
184C ASN 4.0 0.4 - - - -
207C ALA* 4.2 2.2 - - - -
208C ILE 3.1 11.9 - - - -
210C VAL* 3.9 3.7 - - - +
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 3.8 9.2 - - + -
45C LEU* 3.8 30.3 - - + -
46C THR* 4.8 4.5 - - - -
47C ASN* 4.1 7.0 - - - +
89C ILE* 4.4 13.0 - - + -
170C GLY* 3.8 27.8 - - - +
171C GLY 3.5 4.7 - - - +
180C LEU* 4.6 3.4 - - + -
182C GLY* 1.3 74.1 - - - -
184C ASN* 1.3 63.1 + - - +
185C SER* 2.8 17.8 + - - +
207C ALA* 3.1 1.9 - - - -
208C ILE* 2.8 37.7 + - + +
210C VAL* 5.9 0.2 - - - -
213C ALA* 4.0 15.3 - - + -
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Residues in contact with ASN 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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47C ASN* 3.3 1.2 + - - -
119C ALA* 3.6 17.2 - - - +
120C ILE 4.3 3.2 + - - +
164C ILE* 3.4 36.8 - - + +
168C ASN* 4.0 14.1 + - + +
169C SER* 3.2 3.6 - - - -
170C GLY 2.8 29.8 + - - -
171C GLY 2.9 16.8 + - - +
172C ALA 3.1 26.9 + - - -
173C LEU* 3.4 22.8 - - - +
182C GLY 3.9 0.2 + - - -
183C VAL* 1.3 69.3 - - - +
185C SER* 1.3 58.7 + - - +
206C PHE 3.9 4.5 - - - +
207C ALA* 3.8 6.7 - - - +
411F VAL* 4.9 1.1 - - - -
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Residues in contact with SER 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASN* 2.9 27.9 + - - +
49C HIS* 3.4 11.1 - - - -
88C ASP* 4.7 4.3 - - - -
155C LEU* 4.0 22.7 - - - -
164C ILE* 5.5 0.2 - - - +
169C SER* 3.4 15.2 + - - -
183C VAL 2.8 20.4 + - - -
184C ASN* 1.3 71.6 - - - +
186C ALA* 1.3 60.5 + - - +
206C PHE 2.9 11.7 + - - -
208C ILE* 3.3 14.4 - - - +
410F GLN* 3.8 0.9 - - - +
411F VAL* 3.4 12.3 + - - +
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Residues in contact with ALA 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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142C VAL* 4.8 1.6 - - + -
144C THR* 5.2 2.2 - - - -
155C LEU* 4.7 12.3 - - + -
164C ILE* 4.7 1.2 - - - +
185C SER* 1.3 79.3 - - - +
187C ILE* 1.3 65.0 + - - +
206C PHE* 2.7 47.4 + - + +
408F VAL* 4.7 9.6 - - + -
409F GLU 3.2 16.6 - - - +
410F GLN* 4.0 12.6 - - + +
411F VAL* 3.8 6.3 - - - +
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Residues in contact with ILE 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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164C ILE* 3.3 44.9 - - + +
166C PRO* 4.4 2.0 - - + -
186C ALA* 1.3 79.9 - - - +
188C ALA* 1.3 64.7 + - - +
189C THR* 4.2 3.8 - - + -
199C SER 3.6 23.3 - - - +
200C GLY 3.9 17.9 - - - +
201C SER* 4.2 2.9 - - - +
202C ILE 6.1 0.4 - - - +
204C LEU 3.4 10.5 - - - +
205C GLY* 4.1 6.3 - - - -
206C PHE* 4.0 6.7 - - - -
408F VAL* 3.7 2.9 - - - +
409F GLU* 3.0 45.9 + - + +
411F VAL* 3.8 17.2 - - + +
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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