Contacts of the strand formed by residues 116 - 121 (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 PRO 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 6.2 0.4 - - + -
9A GLU* 3.9 11.4 - - - +
114C GLY 3.6 4.9 - - - +
115C GLN* 1.4 96.6 - - + +
117C VAL* 1.3 64.1 + - - +
132C THR* 6.1 0.2 - - - +
133C GLY 3.6 9.2 - - - +
134C ILE* 4.5 4.7 - - + -
175C ASN* 4.1 5.9 - - - -
176C MSE 3.6 38.3 + - + +
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Residues in contact with VAL 117 (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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111C LEU* 5.2 2.2 - - + -
115C GLN* 4.2 1.1 - - + +
116C PRO* 1.3 78.6 - - - +
118C LEU* 1.3 65.8 + - - +
119C ALA 4.4 0.2 + - - -
131C THR 4.0 0.2 - - - +
132C THR* 4.3 0.9 + - - -
133C GLY* 3.0 35.3 + - - +
134C ILE 3.7 15.9 - - - -
135C VAL* 4.0 22.4 - - + +
160C THR* 3.4 26.2 - - - +
162C ALA* 4.7 1.3 - - + -
173C LEU* 3.8 27.6 - - + -
174C VAL 3.3 16.6 - - - +
175C ASN* 4.7 1.8 - - - -
176C MSE 3.7 6.2 - - - +
181C VAL* 4.4 7.6 - - + -
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Residues in contact with LEU 118 (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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134B ILE* 4.7 0.2 - - + -
8C VAL* 3.6 35.7 - - + +
11C VAL* 3.6 26.5 - - + -
12C ALA* 3.9 13.5 - - - +
117C VAL* 1.3 82.2 - - - +
119C ALA* 1.3 60.3 + - - +
120C ILE* 4.5 3.8 - - + -
130C VAL* 4.0 21.3 - - + -
131C THR 3.3 11.4 - - - +
132C THR* 4.0 13.0 - - - +
172C ALA 3.6 1.2 - - - +
173C LEU* 3.3 7.2 - - - +
174C VAL* 2.8 45.3 + - + +
176C MSE 3.5 15.9 - - + +
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Residues in contact with ALA 119 (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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118C LEU* 1.3 73.9 - - - +
120C ILE* 1.3 64.9 + - - +
129C THR 3.5 1.1 - - - +
130C VAL* 3.4 1.6 - - - +
131C THR* 2.9 48.8 + - - +
162C ALA* 3.8 15.6 - - + +
163C ALA 4.6 0.4 - - - +
164C ILE* 4.0 12.3 - - + -
168C ASN* 5.1 4.3 - - - +
172C ALA 3.2 4.9 - - - -
173C LEU* 4.1 4.9 - - + +
184C ASN* 3.6 18.2 - - - +
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Residues in contact with ILE 120 (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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12C ALA* 4.8 6.1 - - - -
15C VAL* 3.7 33.4 - - + -
16C VAL* 4.2 24.2 - - + +
19C VAL* 3.7 28.2 - - + +
118C LEU* 4.5 7.0 - - + +
119C ALA* 1.3 80.4 - - - +
121C GLY* 1.3 60.1 + - - +
128C GLY* 4.8 7.4 - - - -
129C THR 3.2 9.6 - - - +
130C VAL* 4.3 21.3 - - + -
168C ASN* 4.4 3.7 - - - +
171C GLY* 3.7 3.6 - - - -
172C ALA* 2.7 38.5 + - + +
174C VAL* 4.7 8.5 - - + -
184C ASN* 4.3 2.0 + - - +
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Residues in contact with GLY 121 (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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19C VAL* 4.3 6.3 - - - -
34C SER* 3.5 13.9 - - - -
120C ILE* 1.3 78.4 - - - +
122C SER* 1.3 65.0 + - - -
123C PRO* 3.3 7.4 - - - +
126C LEU 3.3 0.7 - - - +
128C GLY 3.2 5.5 + - - -
129C THR 2.9 32.6 + - - -
168C ASN* 3.7 11.0 + - - -
171C GLY* 4.9 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