Contacts of the strand formed by residues 126 - 132 (chain B) in PDB entry 3C3P
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 ILE 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 3.9 9.9 - - + +
60B VAL* 3.6 33.7 - - + -
123B GLN* 3.9 17.5 - - + -
124B ARG 4.5 0.2 - - - -
125B ASP* 1.3 71.0 - - - +
127B ASP* 1.3 57.8 + - - +
128B ILE 3.2 31.6 - - - +
129B LEU* 3.9 10.5 - - + +
145B MSE 3.3 33.7 - - + -
148B CYS* 2.8 30.7 + - + +
149B LEU* 3.7 6.0 - - + -
150B ALA* 2.8 22.5 + - - +
153B ALA* 3.2 12.1 - - - +
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Residues in contact with ASP 127 (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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54B LYS* 3.4 17.3 + - - +
56B PRO* 3.6 18.6 - - + -
57B GLN* 2.8 33.9 + - - +
58B LEU 2.9 20.3 + - - +
125B ASP 3.4 6.0 + - - +
126B ILE* 1.3 74.0 - - - +
128B ILE* 1.3 65.7 + - - +
150B ALA* 3.3 20.2 - - - +
151B LYS 4.8 2.1 - - - +
153B ALA* 3.4 5.3 - - - +
154B LEU 2.9 25.0 + - - -
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Residues in contact with ILE 128 (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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50B LEU 4.8 0.9 - - - +
51B ALA* 4.0 26.0 - - + +
54B LYS* 4.2 14.6 - - + -
56B PRO* 3.9 28.0 - - + -
58B LEU 3.2 4.2 + - - -
59B VAL* 3.4 21.7 - - + +
60B VAL 2.9 26.9 + - - -
73B PHE* 4.1 12.1 - - + -
126B ILE* 3.2 5.4 - - - +
127B ASP* 1.3 83.9 - - - +
129B LEU* 1.3 67.1 + - - +
130B PHE 4.6 0.2 - - - +
154B LEU* 3.3 14.4 - - + +
156B ILE* 3.7 31.0 - - + -
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Residues in contact with LEU 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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60B VAL* 3.7 20.4 - - + +
62B PRO* 4.1 12.8 - - + -
126B ILE* 3.9 2.7 - - + +
128B ILE* 1.3 76.2 - - - +
130B PHE* 1.3 68.8 + - - +
131B MSE 4.5 0.9 - - + -
141B VAL* 4.2 11.4 - - + -
142B LEU* 5.3 3.4 - - + -
145B MSE 4.0 46.2 - - + -
149B LEU* 4.0 29.5 - - + +
154B LEU 3.0 7.9 + - - +
155B LEU* 3.5 24.7 - - + +
156B ILE 3.0 24.6 + - - +
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Residues in contact with PHE 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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39B VAL* 4.0 10.1 - - + -
47B LEU* 3.8 16.8 - - + -
59B VAL* 5.4 0.2 - - + -
60B VAL 3.0 15.0 + - - +
61B VAL* 3.8 20.4 - - + -
62B PRO* 2.9 28.9 - - + +
63B GLY 4.7 8.3 - - - -
64B ASP* 5.2 0.7 - - - -
69B ALA* 3.7 18.8 - - + -
73B PHE* 3.8 34.8 - + + -
128B ILE* 4.0 1.3 - - + -
129B LEU* 1.3 74.7 - - - +
131B MSE 1.3 76.3 + - - +
132B ASP* 4.6 4.9 - - + -
156B ILE* 3.4 14.1 - - + +
158B VAL* 3.6 42.2 - - + -
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Residues in contact with MSE 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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62B PRO* 5.1 5.2 - - + -
129B LEU* 4.5 1.6 - - + -
130B PHE* 1.3 85.5 - - - +
132B ASP* 1.3 68.4 + - - +
133B CYS* 5.2 4.0 - - - -
136B PHE* 4.7 9.0 - - + +
138B GLY* 3.9 28.5 - - - +
141B VAL* 3.7 39.7 - - + -
142B LEU* 5.7 1.3 - - + -
155B LEU* 2.2 54.3 - - + -
156B ILE 2.9 7.8 + - - +
157B ALA* 3.2 14.4 - - - -
158B VAL* 2.9 28.9 + - - +
181B PHE* 4.8 2.0 - - + -
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Residues in contact with ASP 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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37B PRO* 6.1 1.0 - - - +
62B PRO 5.5 2.3 + - - +
63B GLY 5.7 4.3 - - - +
130B PHE* 4.6 6.5 - - + -
131B MSE 1.3 74.1 - - - +
133B CYS* 1.3 59.0 + - - +
134B ASP* 2.8 18.4 + - - +
135B VAL* 2.9 38.3 + - + +
136B PHE* 3.0 20.1 + - + +
158B VAL* 4.0 11.9 - - + +
159B ASN* 2.8 32.1 + - - -
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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