Contacts of the strand formed by residues 125 - 134 (chain B) in PDB entry 3PIJ
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 LEU 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B CYS* 4.1 15.3 - - + -
61B TYR* 3.2 30.2 + - + +
117B ALA* 3.9 13.9 - - + -
118B VAL* 3.3 28.9 - - - +
119B ILE* 3.8 14.4 - - + +
120B ASP* 5.4 0.2 - - - -
124B ASP* 1.3 76.3 - - - +
126B ARG* 1.3 60.1 + - - +
127B PHE* 3.7 28.7 - - + -
152B LEU* 3.6 8.7 - - - +
153B PRO* 3.2 26.0 - - + +
158B LEU* 3.7 34.1 - - + -
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Residues in contact with ARG 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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117B ALA* 3.4 2.2 - - - -
118B VAL* 2.9 36.7 + - - +
120B ASP* 5.2 7.7 + - - +
124B ASP 3.7 1.7 + - - +
125B LEU* 1.3 74.8 - - - +
127B PHE* 1.3 63.8 + - - +
128B TYR* 3.1 33.9 + - + -
150B THR* 3.0 39.1 + - - +
151B ALA 3.8 6.0 + - - +
152B LEU* 3.7 25.3 - - + +
164B GLN* 2.5 33.5 + - - +
214B MET* 4.2 23.4 - - + +
215B VAL* 3.6 21.9 - - - +
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Residues in contact with PHE 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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68B PHE* 3.9 25.4 - + - -
83B TRP* 3.9 22.2 - + + -
100B MET* 3.7 30.7 - - + -
101B PHE* 4.3 17.0 - + + -
116B SER 3.4 4.3 - - - +
117B ALA* 3.7 25.8 - - + -
125B LEU* 3.7 19.7 - - + -
126B ARG* 1.3 74.1 - - - +
128B TYR* 1.3 60.9 + - - +
129B TYR* 4.9 2.9 - - + -
150B THR* 2.8 27.9 + - - -
151B ALA* 2.9 42.2 + - + +
153B PRO* 4.1 19.7 - - + -
158B LEU* 4.3 3.4 - - + -
161B ALA* 4.1 3.1 - - + -
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Residues in contact with TYR 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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83B TRP* 4.4 1.0 - - - -
115B GLY* 3.1 2.1 - - - -
116B SER* 2.8 42.3 + - - +
118B VAL* 3.9 12.6 - - + -
126B ARG* 3.1 29.4 - - + -
127B PHE* 1.3 75.1 - - - +
129B TYR* 1.3 62.5 + - - +
148B GLN* 6.3 0.2 - - + -
149B MET 3.4 3.6 - - - +
150B THR* 3.8 12.1 - - - -
167B ILE* 3.6 29.6 - - + -
182B PRO* 3.8 18.9 - - + +
184B VAL* 3.4 35.0 - - + -
193B MET* 3.7 6.1 - - + -
214B MET* 2.7 44.4 + - - +
217B TRP* 3.5 10.6 - + - -
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 3.7 22.0 - + + -
101B PHE* 4.5 19.3 - + - -
105B LEU* 4.1 0.9 - - - +
108B GLU* 2.7 30.4 + - + -
112B VAL* 3.6 23.1 - - + -
113B PHE 4.0 1.8 - - - +
114B SER 3.5 8.1 - - - +
127B PHE* 4.9 3.1 - - + -
128B TYR* 1.3 79.2 - - - +
130B THR* 1.3 70.9 + - - +
131B GLY 4.6 0.2 - - - -
148B GLN* 3.6 2.3 - - - +
149B MET* 2.7 69.0 + - + +
150B THR 4.4 3.6 + - - -
151B ALA* 4.1 23.6 - - + -
163B LYS* 3.6 24.0 - - - +
165B GLY 5.7 0.3 + - - -
182B PRO* 3.8 6.9 - - - +
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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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112B VAL 4.0 0.2 - - - -
113B PHE* 2.9 42.0 + - + +
114B SER 3.1 10.6 + - - -
129B TYR* 1.3 77.5 - - - +
131B GLY* 1.3 72.0 + - - +
146B GLN* 3.7 16.8 - - + -
147B VAL 3.3 12.1 - - - +
148B GLN* 2.6 17.1 + - - -
179B TYR 4.0 1.6 - - - +
180B ARG* 3.2 21.8 - - + -
181B ASP* 2.9 22.3 + - - -
182B PRO* 3.6 0.9 - - - +
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Residues in contact with GLY 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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107B GLN 3.1 20.0 - - - +
108B GLU* 3.7 17.5 - - - -
129B TYR* 4.8 0.2 - - - -
130B THR* 1.3 73.5 - - - +
132B HIS* 1.3 57.9 + - - -
145B TRP 3.7 0.2 - - - +
146B GLN* 3.3 7.3 - - - -
147B VAL 2.8 35.0 + - - -
149B MET* 3.5 14.1 - - - +
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Residues in contact with HIS 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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78B TRP* 5.2 0.4 - + - -
107B GLN 3.4 1.0 + - - -
108B GLU* 3.5 8.0 - - - +
109B LYS 3.7 0.3 + - - -
110B ASP* 3.2 48.6 + - + +
111B GLY 3.1 12.7 + - - +
113B PHE* 3.4 41.9 - + + -
130B THR 3.9 0.2 + - - -
131B GLY* 1.3 74.6 - - - -
133B ARG* 1.3 78.4 + - - +
134B TRP* 3.4 34.7 - + - -
144B ASP* 3.1 28.0 - - - -
145B TRP 3.9 0.9 - - - -
146B GLN* 3.1 23.1 + - + +
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Residues in contact with ARG 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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106B GLU* 3.6 35.2 + - - +
107B GLN* 3.6 34.6 + - - +
109B LYS* 4.3 14.6 - - + +
110B ASP* 3.3 11.4 - - - +
132B HIS* 1.3 91.0 - - - +
134B TRP* 1.3 63.4 + - - +
145B TRP* 2.7 102.1 + - + +
147B VAL* 3.7 21.6 - - - +
166B MET* 5.0 1.0 - - - -
169B ASP* 4.9 2.8 + - - -
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Residues in contact with TRP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B TRP* 4.2 29.4 - + - -
110B ASP* 2.9 33.7 + - - +
132B HIS* 3.4 25.4 - + - -
133B ARG* 1.3 81.6 - - - +
135B ALA* 1.3 64.5 + - - +
136B ASN* 3.8 0.2 - - - +
137B GLY* 2.9 13.7 + - - -
138B HIS* 3.4 30.7 + - - +
139B ASP* 3.3 47.6 + - - +
140B ASN* 3.5 26.2 - - + -
143B GLY 3.8 3.1 - - - -
144B ASP* 3.3 23.6 - - - -
145B TRP* 4.2 5.3 - - - -
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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