Contacts of the strand formed by residues 126 - 135 (chain A) in PDB entry 3B6R
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 VAL 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.7 23.3 - - + -
122A ASP 3.0 10.5 + - - +
123A PRO* 3.5 13.9 - - - +
125A TYR* 1.3 75.1 - - - +
127A LEU* 1.3 62.3 + - - +
128A SER 3.6 16.6 - - - +
129A SER* 3.7 4.7 - - - +
243A GLY* 3.5 31.3 - - - +
244A GLY* 3.6 14.1 - - - -
295A VAL* 3.8 13.5 - - + -
296A HIS 3.7 3.1 - - - -
297A ILE* 4.3 7.0 - - + +
357A VAL* 4.0 20.2 - - + -
361A ILE* 4.3 4.9 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A PRO 4.6 7.4 - - - +
125A TYR 3.9 6.3 - - - +
126A VAL* 1.3 77.0 - - - +
128A SER* 1.3 64.3 + - - +
242A LYS* 3.4 11.1 + - - +
243A GLY 2.9 16.6 + - - +
296A HIS* 2.8 19.4 + - + +
298A LYS* 3.8 38.4 - - + +
326A ASP* 4.0 30.5 - - + +
330A VAL* 5.6 0.7 - - + -
333A VAL* 4.3 15.0 - - + -
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A VAL* 3.5 2.1 - - - +
127A LEU* 1.3 80.9 - - - +
129A SER* 1.3 60.7 + - - +
240A MET* 6.3 0.4 - - - -
241A GLN 3.3 13.9 - - - -
242A LYS* 4.1 6.1 - - - -
243A GLY 3.3 11.9 - - - -
295A VAL* 3.2 8.9 - - - +
296A HIS* 3.0 53.5 + - - +
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.6 0.7 - - - +
128A SER* 1.3 75.1 + - - +
130A ARG* 1.3 65.6 + - - +
240A MET* 3.2 2.9 - - - +
241A GLN* 2.9 30.5 + - - -
243A GLY 3.1 15.5 + - - -
244A GLY* 3.4 15.3 - - - -
245A ASN 4.7 0.7 - - - -
246A MET* 3.9 24.0 + - - +
249A VAL* 3.7 18.5 - - - +
294A GLY 3.4 4.9 - - - -
295A VAL* 3.7 10.1 - - - +
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Residues in contact with ARG 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A SER* 1.3 76.8 - - - +
131A VAL* 1.3 65.3 + - - +
132A ARG* 5.1 9.2 - - - +
191A HIS 5.7 2.2 + - - -
226A LEU* 6.1 1.4 - - - +
238A ILE* 4.1 28.5 - - - +
239A SER 3.0 15.3 - - - +
240A MET* 3.4 15.7 - - + +
246A MET* 4.2 1.5 - - - +
249A VAL* 3.8 2.9 - - - +
292A ARG* 3.8 31.2 - - - +
293A ALA* 3.3 2.1 - - - +
294A GLY 2.8 46.9 + - - +
296A HIS* 5.6 8.4 + - - -
335A ASP* 4.6 7.9 + - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 1.3 81.5 - - - +
132A ARG* 1.3 64.8 + - - +
238A ILE* 3.5 1.9 - - - -
239A SER 2.9 30.7 + - - -
246A MET* 3.7 23.3 - - - -
249A VAL* 3.9 12.1 - - + -
250A PHE* 4.4 15.3 - - + -
253A PHE* 3.6 30.5 - - + -
291A LEU* 3.6 35.9 - - + -
292A ARG 3.4 3.1 - - - -
293A ALA* 3.9 8.5 - - + -
350A VAL* 4.6 0.9 - - + -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 5.1 12.3 - - - +
131A VAL* 1.3 75.9 - - - +
133A THR* 1.3 67.9 + - - +
236A ARG* 4.0 26.6 - - - +
237A VAL 3.0 12.3 - - - +
238A ILE* 3.4 24.9 - - + -
253A PHE* 3.9 3.4 - - - -
286A ASN* 4.5 15.0 - - - +
290A GLY 3.2 22.0 + - - -
291A LEU* 3.2 6.8 - - - +
292A ARG* 2.9 77.5 + - + +
341A ARG* 4.0 12.7 - - - +
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 1.3 82.1 - - - +
134A GLY* 1.3 67.2 + - - +
135A ARG* 2.9 27.1 + - + +
236A ARG* 3.4 7.5 + - - +
237A VAL* 2.8 39.1 + - + +
253A PHE* 3.5 27.8 - - + -
257A LEU* 4.1 7.6 - - + -
289A THR 2.6 28.0 + - - -
290A GLY 3.1 10.3 + - - -
291A LEU* 4.5 1.1 - - - -
346A GLU* 6.5 0.2 - - - -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 1.3 77.6 + - - +
135A ARG* 1.3 83.6 + - - -
233A ASP* 5.2 2.2 - - - -
235A LEU 3.2 11.2 - - - -
236A ARG* 4.3 4.9 - - - -
237A VAL 4.8 0.4 - - - -
279A TYR* 4.6 2.1 - - - +
281A LEU* 3.4 29.5 - - - +
290A GLY 3.9 4.0 + - - -
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Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.2 9.1 - - - +
133A THR* 2.9 24.8 + - + +
134A GLY* 1.3 99.9 + - - -
136A SER* 1.3 62.5 + - - +
234A HIS* 3.5 6.3 + - - +
235A LEU* 2.9 43.7 + - + +
237A VAL* 5.2 3.6 - - + -
253A PHE* 5.1 1.0 - - - -
257A LEU* 3.6 35.8 - - + +
271A PHE* 3.6 49.4 - - + -
279A TYR* 3.3 56.9 - - - +
281A LEU* 3.5 6.6 - - - +
289A THR 4.0 1.8 + - - -
346A GLU* 4.3 6.3 + - - +
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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