Contacts of the strand formed by residues 128 - 135 (chain A) in PDB entry 1NNC
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 GLU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A SER 4.5 0.2 - - - +
125A ASP* 2.7 42.9 + - + +
127A ASP* 1.3 91.6 - - - +
129A CYS* 1.3 70.7 + - - +
130A ARG* 3.2 42.3 + - + +
162A PRO* 4.7 8.8 - - - +
172A ARG* 5.0 4.0 + - - -
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Residues in contact with CYS 129 (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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100A TYR* 3.3 28.0 - - + +
122A VAL* 4.8 3.8 - - + -
123A SER 3.7 4.9 - - - +
124A CYS* 2.0 45.8 - - - -
125A ASP 5.2 0.2 - - - -
128A GLU* 1.3 83.1 - - - +
130A ARG* 1.3 61.3 + - - +
163A LEU* 3.6 27.9 + - + +
412A ASP* 4.1 17.5 - - - -
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Residues in contact with ARG 130 (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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122A VAL* 3.4 6.5 - - - +
123A SER 3.0 30.8 + - - +
125A ASP* 4.9 10.1 - - - -
128A GLU* 3.2 43.0 + - + +
129A CYS* 1.3 79.0 - - - +
131A PHE* 1.3 66.1 + - - +
132A TYR* 3.4 23.2 - - + -
160A SER* 3.1 44.0 + - - -
161A TRP* 3.3 19.0 - - - +
162A PRO* 4.0 17.5 - - + +
163A LEU* 4.4 2.0 - - - +
170A ASN 4.8 2.4 + - - -
172A ARG* 3.4 41.4 - - - +
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Residues in contact with PHE 131 (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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101A GLY* 4.1 20.4 - - - -
103A ASP* 3.9 17.0 - - + -
121A TYR 3.7 1.8 - - - -
122A VAL* 3.8 26.9 - - + -
130A ARG* 1.3 74.7 - - - +
132A TYR* 1.3 59.0 + - - +
160A SER* 3.1 6.2 - - - -
161A TRP* 2.9 68.2 + - + +
163A LEU* 3.3 28.2 - - + +
164A SER* 3.4 31.0 - - - -
165A SER 4.2 0.4 - - - -
443A ILE* 3.7 31.4 - - + -
445A SER* 4.3 5.6 - - - -
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Residues in contact with TYR 132 (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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120A PRO* 3.0 7.0 - - - +
121A TYR* 2.8 59.0 + + + +
122A VAL 4.4 0.4 - - - -
123A SER* 3.5 28.7 + - - -
125A ASP* 4.3 2.4 + - - -
130A ARG* 3.4 34.7 - - + -
131A PHE* 1.3 76.5 - - - +
133A ALA* 1.3 62.8 + - - +
158A LEU* 4.1 14.1 - - + -
159A ILE 3.3 8.5 - - - -
160A SER* 3.5 24.2 + - - -
161A TRP* 3.5 5.5 - - - -
172A ARG* 5.5 1.0 + - - -
174A GLU* 4.2 14.7 + - + -
182A SER* 4.0 14.8 - - - -
189A ARG* 3.2 34.0 + - - -
443A ILE* 4.5 0.3 - - - +
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Residues in contact with ALA 133 (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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117A THR* 3.9 21.8 - - + +
118A ARG 4.0 1.1 - - - +
119A GLU 3.9 9.9 - - - -
120A PRO* 3.8 13.9 - - + -
121A TYR* 5.1 0.2 - - - -
132A TYR* 1.3 78.1 - - - +
134A LEU* 1.3 64.5 + - - +
135A SER 3.8 0.2 - - - -
157A ALA 3.5 0.7 - - - +
158A LEU* 3.4 7.5 - - - +
159A ILE* 2.9 34.0 + - - +
161A TRP* 3.4 21.3 - - + -
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Residues in contact with LEU 134 (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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117A THR* 3.3 2.7 - - - -
118A ARG 3.1 21.9 + - - +
119A GLU* 3.7 22.1 + - + +
133A ALA* 1.3 74.4 - - - +
135A SER* 1.3 62.5 + - - +
156A ARG* 2.9 34.4 + - + +
157A ALA 3.4 0.9 - - - -
158A LEU* 3.9 20.6 - - + +
177A GLY 4.0 20.4 - - - +
178A TRP* 3.3 29.6 - - - +
179A SER 3.8 2.7 - - - +
180A SER* 3.8 25.1 - - - +
227A GLU* 3.9 16.4 - - - +
479A ZMR 4.2 2.0 - - - +
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Residues in contact with SER 135 (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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115A LEU* 4.2 14.0 - - - +
116A VAL 3.5 10.4 + - - -
117A THR* 4.1 4.5 - - - +
133A ALA 3.7 2.6 + - - -
134A LEU* 1.3 72.7 - - - +
136A GLN* 1.3 62.1 + - - +
137A GLY* 2.8 17.5 + - - -
155A TYR 5.2 0.2 - - - -
156A ARG* 3.0 32.0 + - - +
157A ALA* 2.8 22.2 + - - -
159A ILE* 4.1 25.3 - - - +
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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