Contacts of the strand formed by residues 129 - 135 (chain B) in PDB entry 1NUS
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.3 31.8 - - + +
6B PRO 2.6 12.4 + - - +
7B VAL* 3.3 7.9 - - + +
8B VAL* 2.9 24.8 + - - -
39B TYR* 3.5 17.7 + - - -
127B VAL 4.9 3.6 - - - +
128B PRO* 1.3 72.7 - - - +
130B LEU* 1.3 59.3 + - - +
131B LYS* 3.1 31.9 + - - +
160B PHE 5.4 3.4 - - - +
188B ASN* 5.6 2.5 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.6 32.3 - - + +
10B LEU* 4.2 18.6 - - + -
45B ILE* 5.6 1.1 - - + -
97B LEU* 3.1 43.7 - - + +
100B HIS* 3.9 14.1 - - + +
101B HIS* 3.6 25.4 + - + +
104B LEU* 3.9 15.5 - - + -
128B PRO 3.7 1.8 + - - -
129B GLU* 1.3 72.9 - - - +
131B LYS* 1.3 59.9 + - - +
160B PHE* 3.0 39.7 + - + +
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B VAL* 3.8 22.9 - - + -
8B VAL 3.0 10.3 + - - +
9B LEU* 3.5 7.6 - - + -
10B LEU* 2.9 26.9 + - - +
33B LEU* 4.7 2.9 - - + -
39B TYR* 3.8 19.9 + - - -
97B LEU* 4.6 3.8 - - - -
129B GLU* 3.1 30.3 + - - +
130B LEU* 1.3 78.8 - - - +
132B LEU* 1.3 60.6 + - - +
160B PHE 3.7 13.7 + - - +
161B GLY* 3.4 19.8 - - - +
163B VAL* 4.1 26.9 - - + -
188B ASN* 4.7 8.7 - - - +
190B HIS* 3.9 20.8 + - + -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 3.5 15.0 - - + +
12B CYS* 4.4 16.2 - - + +
93B THR* 3.9 31.2 - - + -
97B LEU* 4.3 24.8 - - + +
131B LYS* 1.3 70.7 - - - +
133B LEU* 1.3 66.7 + - - +
134B CYS* 5.1 6.1 - - + -
138B VAL* 5.8 2.5 - - + -
142B PHE* 5.2 4.9 - - + -
148B TRP* 5.4 4.9 - - + -
156B ILE* 4.1 19.5 - - + -
161B GLY 2.8 15.5 + - - +
162B LEU* 3.5 23.5 - - + +
163B VAL* 2.9 26.4 + - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.4 13.5 - - + -
10B LEU 2.6 25.3 + - - +
11B ALA* 3.6 12.6 - - - +
12B CYS 4.4 4.0 + - - +
25B MET* 3.9 25.7 - - + +
26B PHE* 3.6 55.6 - - + -
29B ALA* 3.6 27.4 - - + -
131B LYS 3.6 0.6 + - - -
132B LEU* 1.3 74.8 - - - +
134B CYS* 1.3 70.9 - - - +
163B VAL* 3.4 17.5 - - + +
165B VAL* 4.1 4.7 - - + -
502B APC 4.3 2.3 + - - -
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Residues in contact with CYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B CYS 6.0 0.4 - - - +
25B MET* 3.9 8.8 - - - +
132B LEU* 5.1 5.6 - - + -
133B LEU* 1.3 78.5 - - - +
135B GLY* 1.3 71.1 + - - +
138B VAL* 3.8 25.6 - - + -
139B LEU* 4.6 6.3 - - - -
142B PHE* 5.6 0.4 - - - -
162B LEU* 3.7 31.4 - - - -
163B VAL 3.0 9.1 + - - +
164B CYS* 3.2 12.5 - - - -
165B VAL* 2.9 23.9 + - - +
502B APC 3.2 13.5 - - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B MET* 4.0 2.1 - - - -
134B CYS* 1.3 78.8 - - - +
136B ALA* 1.3 67.2 + - - +
137B ASP* 3.1 5.8 - - - -
138B VAL* 2.9 18.9 + - - +
139B LEU 3.6 2.6 + - - -
164B CYS* 4.0 1.6 - - - -
165B VAL 3.5 9.0 - - - -
167B ARG* 4.3 6.5 - - - -
502B APC 3.0 31.7 + - - -
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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