Contacts of the strand formed by residues 125 - 130 (chain B) in PDB entry 3C6Q
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B GLY* 1.3 74.6 - - - -
126B VAL* 1.3 62.3 + - - +
155B GLU* 3.3 21.1 - - - +
157B VAL* 3.7 30.1 - - + -
180B HIS* 5.6 6.4 + - + +
182B ASP* 2.8 46.1 + - - +
183B LEU* 3.3 7.6 - - + +
184B ASP* 2.7 41.6 + - - +
185B ALA 3.1 6.8 + - - -
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Residues in contact with VAL 126 (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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116B MET* 4.3 9.4 - - + -
120B LEU* 3.9 24.9 - - + -
125B LYS* 1.3 79.8 - - - +
127B VAL* 1.3 80.3 + - - +
128B ILE* 4.3 7.4 - - + -
145B PHE* 4.2 24.5 - - + -
154B ILE* 4.0 15.0 - - + -
155B GLU 2.7 13.6 + - - +
156B ILE* 3.4 11.1 - - + +
157B VAL* 2.8 30.0 + - - +
158B ASP 3.9 0.7 + - - -
185B ALA* 3.4 13.2 - - + +
187B PHE* 4.5 4.9 - - + -
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Residues in contact with VAL 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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126B VAL* 1.3 77.0 - - - +
128B ILE* 1.3 66.2 + - - +
157B VAL* 3.5 24.0 - - + -
158B ASP* 3.8 12.3 - - + +
160B LEU* 3.7 28.7 - - + -
176B ALA* 4.0 16.2 - - + -
180B HIS* 4.0 6.7 - - + -
183B LEU* 3.5 14.3 - - + +
185B ALA 2.9 7.3 + - - -
186B PHE* 3.2 32.9 - - + -
187B PHE 2.9 23.4 + - - -
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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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126B VAL* 4.3 11.0 - - + -
127B VAL* 1.3 84.2 - - - +
129B GLY* 1.3 63.5 + - - +
130B THR 4.4 0.7 - - - +
142B ILE* 4.1 23.6 - - + -
145B PHE* 4.4 4.5 - - + -
156B ILE* 4.1 25.1 - - + -
158B ASP 3.1 13.8 + - - +
159B ILE* 4.1 23.1 - - + -
160B LEU* 2.9 28.1 + - - +
187B PHE* 3.3 36.3 - - + +
189B VAL* 4.0 15.9 - - + -
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Residues in contact with GLY 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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128B ILE* 1.3 73.5 - - - +
130B THR* 1.3 59.3 + - - -
160B LEU* 3.9 9.6 - - - -
162B ASP* 5.1 0.7 - - - -
186B PHE* 6.0 0.2 - - - -
187B PHE 2.8 11.7 + - - +
188B GLY* 3.4 1.4 - - - -
189B VAL* 2.9 26.0 + - - +
193B ASN* 3.0 21.8 - - - -
197B GLN* 3.6 11.5 - - - +
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Residues in contact with THR 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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128B ILE* 4.4 0.7 - - + -
129B GLY* 1.3 75.1 - - - -
131B GLY* 1.3 66.7 + - - +
132B SER 3.3 14.6 + - - +
133B LEU* 4.7 6.1 - - + -
138B SER* 2.7 23.9 + - - -
142B ILE* 4.0 18.2 - - + -
159B ILE* 4.2 15.3 - - + -
160B LEU 3.1 24.0 + - - +
161B ASN* 3.7 1.9 - - - -
162B ASP* 3.2 17.8 + - - +
189B VAL* 3.7 21.5 - - - +
190B TYR* 4.7 0.7 - - - -
193B ASN* 3.6 8.7 - - - -
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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