Contacts of the strand formed by residues 131 - 137 (chain B) in PDB entry 3U4S
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 131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B PRO* 3.8 29.2 - - + -
71B ILE 3.4 8.5 - - - +
72B GLN* 4.3 18.6 - - + +
89B LYS* 5.1 12.3 - - + -
92B MET* 4.4 12.3 - - + -
97B PHE* 3.2 15.4 - - + -
100B ILE* 5.0 10.1 - - + -
106B TYR* 3.7 28.9 - - + +
129B PRO 4.9 0.4 - - - +
130B PRO* 1.3 81.5 - - - +
132B TYR* 1.3 61.0 + - - +
180B MET* 3.2 38.0 - - + +
183B THR* 3.7 2.2 - - - -
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Residues in contact with TYR 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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70B PRO* 3.5 2.0 - - - +
71B ILE* 2.8 52.8 + - + +
73B GLN* 3.7 22.7 - - - -
97B PHE* 4.3 1.3 - - - -
130B PRO 4.3 0.2 - - - -
131B ILE* 1.3 73.2 - - - +
133B GLY* 1.3 60.4 + - - +
134B ALA* 3.0 23.7 + - + -
177B TYR* 3.7 18.5 - + + +
178B PHE 3.3 15.7 - - - -
179B GLY* 3.5 17.0 - - - -
183B THR* 3.8 14.8 - - + +
184B SER 4.0 12.3 - - - -
185B PHE* 5.2 1.1 - - + -
206B LYS* 3.4 6.8 + - - -
280B ASN* 3.1 30.2 + - - -
503B 08P 2.5 34.5 + - + -
11D CYS* 5.8 4.5 - - + -
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Residues in contact with GLY 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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67B ILE* 3.8 22.7 - - - -
70B PRO* 4.7 2.0 - - - -
97B PHE* 3.8 12.0 - - - -
132B TYR* 1.3 69.6 - - - +
134B ALA* 1.3 62.5 + - - +
136B VAL* 3.5 14.0 - - - +
177B TYR* 3.6 1.0 - - - -
178B PHE* 2.9 42.8 + - - -
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Residues in contact with ALA 134 (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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67B ILE* 4.8 1.2 - - - +
68B PRO* 5.9 0.3 - - - +
69B ALA* 4.6 12.1 + - - +
71B ILE* 4.4 12.3 - - + -
132B TYR* 3.0 26.9 + - + +
133B GLY* 1.3 78.6 - - - +
135B ASP* 1.3 79.9 + - - +
136B VAL* 3.1 8.2 + - - +
176B LEU 3.8 0.2 - - - -
177B TYR* 3.4 27.8 - - + +
11D CYS* 4.9 3.4 - - + -
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Residues in contact with ASP 135 (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 PRO* 5.7 1.0 - - - +
71B ILE* 5.7 0.3 - - - +
134B ALA* 1.3 78.3 - - - +
136B VAL* 1.3 59.7 + - - +
137B ASN* 3.7 5.0 + - - -
175B TYR* 3.6 33.4 - - + -
176B LEU 3.5 1.8 + - - -
177B TYR* 3.0 32.0 + - - -
8D ARG* 3.9 20.6 + - - +
10D SER* 3.6 8.2 + - - -
11D CYS* 2.8 36.8 + - - +
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Residues in contact with VAL 136 (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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65B LEU* 4.3 11.9 - - + -
66B VAL 3.8 19.5 - - - +
67B ILE* 3.7 22.9 - - + -
68B PRO* 4.3 12.6 - - + -
133B GLY 3.5 22.7 - - - +
134B ALA 3.6 5.8 - - - +
135B ASP* 1.3 73.5 - - - +
137B ASN* 1.3 73.9 + - - +
138B GLY 3.2 0.3 + - - -
175B TYR* 3.2 4.5 - - - -
176B LEU* 2.7 48.0 + - + +
178B PHE* 4.4 8.1 - - + -
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Residues in contact with ASN 137 (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 PRO* 5.9 1.0 - - - +
135B ASP 3.7 4.8 + - - -
136B VAL* 1.3 81.1 - - - +
138B GLY* 1.3 57.7 + - - +
169B GLU* 3.2 41.4 + - - +
173B THR* 4.3 4.9 + - - -
174B PRO 3.9 5.3 - - - +
175B TYR* 3.5 20.5 + - - -
8D ARG* 5.4 4.0 - - - +
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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