Contacts of the strand formed by residues 138 - 142 (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 SER 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL 3.6 1.4 - - - +
134B ALA* 3.3 2.6 - - - -
135B SER 2.9 32.2 + - - +
136B ARG 3.3 2.7 - - - -
137B GLY* 1.3 81.8 - - - +
139B THR* 1.3 74.1 + - - +
140B SER* 4.8 4.6 + - - -
151B ARG* 5.0 7.3 - - - +
152B PHE 3.7 11.8 + - - -
158B GLY 3.4 1.5 + - - +
159B GLY* 3.7 5.4 - - - -
161B ARG* 4.1 9.6 - - - -
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.6 24.9 - - + -
133B VAL 3.4 4.7 - - - +
134B ALA* 3.5 5.4 - - + +
138B SER* 1.3 75.1 + - - +
140B SER* 1.3 64.9 + - - +
151B ARG* 3.5 2.9 - - - -
152B PHE* 3.0 69.9 + - + -
154B SER* 2.5 29.4 + - - +
156B LEU* 5.1 1.3 - - + -
159B GLY* 3.0 14.6 + - - -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 3.4 2.4 - - - +
132B ILE* 3.4 1.8 - - - +
133B VAL* 2.8 41.7 + - - +
138B SER* 4.3 4.2 + - - -
139B THR* 1.3 75.7 - - - +
141B ALA* 1.3 59.9 + - - +
142B TYR* 3.7 26.8 + - - -
148B CYS* 4.7 1.6 - - - -
150B ASN 3.6 5.6 - - - -
151B ARG* 3.1 33.4 + - - +
152B PHE* 4.5 2.0 - - - -
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Residues in contact with ALA 141 (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* 4.3 8.3 - - + -
131B LEU 3.4 4.3 - - - -
132B ILE* 3.6 19.5 - - + -
140B SER* 1.3 73.8 - - - +
142B TYR* 1.3 61.7 + - - +
148B CYS* 3.6 3.5 - - - -
149B VAL* 2.9 31.0 + - + +
150B ASN 3.1 12.7 + - - +
152B PHE* 4.1 5.6 - - + -
183B TYR* 3.4 27.6 - - + +
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Residues in contact with TYR 142 (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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98B TYR* 3.6 66.8 + + + +
130B ALA* 3.0 10.5 - - - +
131B LEU* 2.8 43.9 + - + +
133B VAL* 4.2 9.4 - - + -
140B SER* 3.7 27.0 + - - -
141B ALA* 1.3 74.5 - - - +
143B THR* 1.3 69.0 + - - +
146B GLY 3.7 20.0 - - - -
147B TYR 3.4 6.3 - - - +
148B CYS* 3.9 24.2 - - + -
149B VAL* 4.7 1.3 - - - -
151B ARG* 3.3 20.7 + - - -
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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