Contacts of the strand formed by residues 128 - 135 (chain B) in PDB entry 3NC0
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 LYS 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A ILE* 4.4 5.7 + - - +
623A CYS* 3.6 26.7 + - - +
625A LEU 4.0 18.8 + - - -
626A GLN 5.9 0.2 - - - -
627A PRO* 5.8 6.1 - - - -
630A VAL* 5.4 6.4 - - - +
127B GLY* 1.3 75.5 + - - +
129B ARG* 1.3 68.9 + - - +
130B ALA* 3.4 4.5 + - + +
149B VAL* 5.2 18.6 - - + -
175B ILE* 3.1 5.4 - - - +
176B TYR* 2.6 55.2 + - + +
178B GLU* 5.2 14.4 + - + +
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Residues in contact with ARG 129 (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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623A CYS 5.2 0.8 + - - -
624A ASP* 4.8 7.8 + - - +
102B LEU* 3.5 29.9 - - + +
103B MET 3.2 26.0 + - - -
104B LEU* 4.0 15.4 - - - +
105B SER* 4.9 7.7 + - - +
127B GLY 4.2 1.4 + - - -
128B LYS* 1.3 74.5 - - - +
130B ALA* 1.3 59.0 + - - +
143B THR* 4.0 17.0 - - - -
144B LYS* 4.1 28.7 + - + +
173B ASP* 3.1 31.8 + - - -
174B CYS 3.3 8.5 - - - -
175B ILE* 4.4 14.0 - - + +
186B LEU* 3.7 24.6 - - - +
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Residues in contact with ALA 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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102B LEU* 3.8 17.7 - - - +
128B LYS* 4.2 7.6 - - + +
129B ARG* 1.3 74.8 - - - +
131B LEU* 1.3 61.4 + - - +
132B ILE* 3.9 2.9 - - + -
141B ALA* 4.3 17.7 - - + -
142B TYR 3.0 15.3 - - - +
143B THR* 4.6 0.9 - - - +
149B VAL* 6.2 2.9 - - + -
172B LEU 3.8 0.5 - - - +
174B CYS 2.8 33.2 + - - +
176B TYR* 5.6 0.7 - - + -
183B TYR* 4.6 13.0 - - + -
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Residues in contact with LEU 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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65B LEU* 4.0 17.3 - - + -
98B TYR* 4.1 18.8 - - + +
101B GLN* 3.6 37.5 - - + -
102B LEU* 3.6 26.0 - - + +
130B ALA* 1.3 70.5 - - - +
132B ILE* 1.3 62.0 + - - +
133B VAL* 4.1 16.4 - - + -
140B SER 3.4 5.2 - - - +
141B ALA* 4.3 0.4 - - - -
142B TYR* 2.8 41.0 + - + +
143B THR* 5.1 2.2 - - - +
171B ILE* 4.2 9.9 - - + -
172B LEU 3.7 1.3 - - - +
189B MET* 3.7 18.2 - - + -
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Residues in contact with ILE 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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130B ALA* 4.8 2.0 - - + +
131B LEU* 1.3 72.8 - - - +
133B VAL* 1.3 64.6 + - - +
134B ALA* 4.8 1.6 - - + +
139B THR* 3.6 23.8 - - + -
140B SER 3.4 1.6 - - - -
141B ALA* 3.6 17.0 - - + -
152B PHE* 4.5 4.5 - - + -
156B LEU* 5.0 12.8 - - + -
170B THR 3.7 0.6 - - - +
171B ILE* 3.3 7.6 - - - +
172B LEU* 2.9 47.3 + - + +
174B CYS* 3.6 30.1 - - + -
183B TYR* 3.5 41.3 - - + -
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Residues in contact with VAL 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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65B LEU* 3.8 23.3 - - + +
66B ALA* 4.1 6.1 - - + -
98B TYR* 4.5 7.9 - - + +
131B LEU* 4.1 25.6 - - + +
132B ILE* 1.3 77.9 - - - +
134B ALA* 1.3 60.9 + - - +
135B SER* 3.7 19.1 + - - +
138B SER 3.6 2.3 - - - +
139B THR* 3.4 2.7 - - - -
140B SER* 2.8 39.3 + - - +
142B TYR* 4.2 18.4 - - + -
170B THR 3.6 5.2 - - - +
171B ILE* 4.6 11.0 - - + -
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Residues in contact with ALA 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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132B ILE* 4.1 1.1 - - + -
133B VAL* 1.3 70.2 - - - +
135B SER* 1.3 63.4 + - - +
138B SER 3.3 5.2 - - - -
139B THR* 3.5 22.0 - - + +
156B LEU* 4.0 21.1 - - + -
157B PRO 3.8 2.9 - - - +
158B GLY 3.5 3.6 - - - -
159B GLY* 3.8 13.5 - - - +
169B TYR* 3.2 4.6 - - - -
170B THR* 2.9 44.7 + - - +
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Residues in contact with SER 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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66B ALA* 2.7 36.5 + - - -
67B GLU* 5.8 0.7 - - - -
133B VAL* 3.7 9.8 + - - +
134B ALA* 1.3 75.5 - - - +
136B ARG* 1.3 73.6 + - - +
137B GLY 3.1 4.2 + - - -
138B SER* 2.9 20.0 + - - +
158B GLY* 3.1 7.1 + - - -
168B ASP 5.1 0.9 - - - -
169B TYR* 3.6 22.0 - - - +
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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