Contacts of the strand formed by residues 116 - 121 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A GLY 3.5 5.3 - - - +
115A GLN* 1.4 94.4 - - + +
117A VAL* 1.3 66.2 + - - +
132A THR* 6.0 1.3 - - - +
133A GLY 3.3 10.5 - - - +
134A ILE* 4.2 5.4 - - + -
175A ASN* 4.2 0.7 - - - -
176A MSE 3.6 45.9 + - + +
8B VAL* 6.0 0.4 - - + -
9B GLU* 3.7 13.2 - - - +
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.1 2.5 - - + -
115A GLN* 4.2 1.6 - - + +
116A PRO* 1.3 79.6 - - - +
118A LEU* 1.3 58.6 + - - +
119A ALA 4.3 0.3 + - - -
132A THR* 3.6 4.9 + - - -
133A GLY 2.9 34.8 + - - +
134A ILE 3.8 15.0 - - - -
135A VAL* 4.1 19.7 - - + +
160A THR* 3.4 26.7 - - - +
162A ALA* 4.5 1.0 - - + +
173A LEU* 3.8 26.2 - - + -
174A VAL 3.1 17.3 - - - +
175A ASN* 4.6 3.6 - - + -
176A MSE 3.9 6.5 - - - -
181A VAL* 4.4 9.9 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.6 27.8 - - + +
11A VAL* 3.9 22.9 - - + -
12A ALA* 4.0 13.5 - - - +
15A VAL* 6.4 0.2 - - + -
117A VAL* 1.3 74.8 - - - +
119A ALA* 1.3 60.2 + - - +
120A ILE* 4.0 8.7 - - + +
130A VAL* 3.9 21.1 - - + -
131A THR 3.2 9.2 - - - +
132A THR* 3.1 27.4 - - - +
172A ALA 3.6 1.0 - - - +
173A LEU* 3.4 5.5 - - - +
174A VAL* 2.7 49.0 + - + +
176A MSE 3.6 15.7 - - + -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 1.3 73.2 - - - +
120A ILE* 1.3 61.1 + - - +
129A THR 3.5 1.3 - - - +
130A VAL* 3.4 5.5 - - - +
131A THR* 2.9 48.5 + - - +
162A ALA* 3.8 15.4 - - + +
163A ALA 4.3 0.2 - - - +
164A ILE* 4.0 14.1 - - + -
168A ASN* 5.0 4.5 - - - +
172A ALA 3.3 4.9 - - - -
173A LEU* 4.2 4.3 - - + -
184A ASN* 3.6 17.5 - - - +
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Residues in contact with ILE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 6.0 0.9 - - - -
15A VAL* 3.8 16.6 - - + -
16A VAL* 4.3 20.6 - - + -
19A VAL* 3.8 32.9 - - + +
118A LEU* 4.0 11.4 - - + +
119A ALA* 1.3 78.2 - - - +
121A GLY* 1.3 62.0 + - - +
128A GLY* 4.7 7.9 - - - -
129A THR 3.3 9.2 - - - +
130A VAL* 4.1 16.4 - - + -
168A ASN* 4.4 3.9 - - - +
171A GLY* 3.6 4.7 - - - -
172A ALA* 2.8 36.3 + - + +
174A VAL* 3.7 39.7 - - + -
184A ASN* 4.5 2.0 + - - -
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 4.3 7.0 - - - -
34A SER* 3.5 14.6 - - - -
120A ILE* 1.3 77.4 - - - +
122A SER* 1.3 61.4 + - - -
123A PRO* 3.4 9.0 - - - +
128A GLY 3.3 6.1 + - - -
129A THR 2.9 32.7 + - - -
168A ASN* 3.8 11.0 + - - -
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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