Contacts of the strand formed by residues 150 - 155 (chain B) in PDB entry 3N1P
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 ALA 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B MET* 5.9 0.3 - - - +
107B CYS* 4.6 0.9 - - - -
132B GLY 3.6 11.4 - - - +
133B TRP 4.4 0.2 + - - -
144B LEU* 3.3 26.3 + - + +
145B HIS* 3.5 16.3 + - + +
148B GLY 3.5 2.2 + - - -
149B ARG* 1.3 82.5 + - - +
151B VAL* 1.3 73.3 + - - +
187B HIS* 3.7 23.8 - - + -
188B CYS 3.0 12.8 - - - +
189B SER* 3.9 2.7 - - - -
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B MET* 4.3 16.2 - - + -
107B CYS* 4.1 13.9 - - - -
111B LEU* 4.1 11.2 - - + -
129B VAL* 4.5 7.9 - - + -
131B GLU 3.0 12.6 - - - +
132B GLY* 3.9 9.4 - - - -
145B HIS* 3.7 2.0 - - - -
150B ALA* 1.3 80.7 - - - +
152B ASP* 1.3 64.0 + - - +
153B ILE* 3.9 18.5 + - + -
175B PHE* 4.1 15.0 - - + -
186B VAL 3.5 2.9 - - - +
187B HIS* 3.6 1.7 + - - -
188B CYS* 2.8 55.1 + - + +
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.6 3.1 - - - +
130B THR* 2.8 50.3 + - - +
131B GLU* 2.9 30.2 + - + +
139B HIS* 4.1 5.2 - - - -
145B HIS* 3.7 5.7 + - - -
151B VAL* 1.3 70.5 - - - +
153B ILE* 1.3 56.8 + - - +
185B HIS* 3.3 31.3 + - + -
186B VAL 3.3 3.2 - - - +
187B HIS* 3.3 6.6 + - - -
194B ZN 2.3 35.5 - - - -
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Residues in contact with ILE 153 (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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111B LEU* 4.4 4.7 - - + -
114B LEU* 3.8 22.9 - - + -
127B LEU* 4.0 14.1 - - + -
128B ARG 3.2 11.0 - - - +
129B VAL* 4.2 9.0 - - + -
151B VAL* 4.1 24.2 - - + +
152B ASP* 1.3 78.2 - - - +
154B THR* 1.3 68.7 + - - +
163B TYR* 5.0 0.2 - - - -
166B LEU* 4.1 19.5 - - + +
170B ALA* 4.5 2.0 - - + -
185B HIS* 3.5 0.5 - - - -
186B VAL* 2.9 53.4 + - + +
188B CYS* 3.4 24.7 - - - -
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.0 5.0 - - - +
128B ARG* 2.8 68.3 + - - +
130B THR* 3.9 10.5 - - + -
153B ILE* 1.3 81.0 - - - +
155B THR* 1.3 64.5 + - - +
163B TYR* 3.2 20.4 - - - +
166B LEU* 3.7 17.9 - - - +
184B ALA 3.1 27.6 - - - +
185B HIS* 4.0 3.1 - - + -
756C ASP* 5.4 0.7 - - - +
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Residues in contact with THR 155 (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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118B VAL* 5.0 1.9 - - - +
122B TRP* 4.2 12.6 - - - -
125B VAL* 3.1 29.9 - - + +
126B LYS 4.0 3.3 + - - -
127B LEU* 5.3 0.2 - - - +
128B ARG* 4.2 0.2 - - - -
154B THR* 1.3 77.7 + - - +
156B SER* 1.3 53.7 + - - +
157B ASP* 2.7 28.6 + - - +
158B ARG* 2.5 35.2 + - - -
162B LYS* 3.9 21.1 - - + +
163B TYR* 3.8 16.2 - - - -
166B LEU* 4.1 11.8 - - - +
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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
------------------------------------------------------------
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