Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 3SOQ
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 PRO 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ASP* 4.3 4.3 - - - +
112A THR* 4.0 24.0 + - + -
113A ASP 3.6 23.3 - - - +
114A SER* 3.7 20.1 - - - -
117A ASN* 4.5 1.6 - - - +
118A ARG 4.5 5.6 - - - +
119A ILE* 5.0 1.1 - - + -
137A LEU* 4.3 26.5 - - + -
138A ASP 3.3 16.4 - - - +
139A GLN* 1.3 91.2 - - - +
141A ARG* 1.3 59.4 + - - +
154A TRP* 4.8 2.9 - - + -
155A THR 3.3 11.7 - - - +
156A ASP* 3.8 4.2 - - - +
157A TRP* 4.7 0.5 + - - -
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Residues in contact with ARG 141 (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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98A ASP* 4.2 21.4 + - - +
99A GLY* 3.3 13.1 - - - -
112A THR* 2.9 23.0 + - - +
140A PRO* 1.3 74.9 - - - +
142A ALA* 1.3 67.8 + - - +
155A THR* 2.9 17.6 + - - +
157A TRP* 3.2 36.3 - - + +
185A ASN* 3.0 46.0 + - - +
228A PHE* 3.7 30.2 - - + -
242A TRP* 4.3 0.8 - - - -
40Z ASN* 2.7 38.1 + - - +
42Z ILE* 3.6 25.4 - - - +
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Residues in contact with ALA 142 (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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99A GLY* 5.0 2.7 - - - -
112A THR* 5.0 0.2 - - - -
141A ARG* 1.3 81.4 - - + +
143A ILE* 1.3 58.8 + - - +
154A TRP* 3.0 9.5 - - - +
155A THR* 3.0 34.2 + - + +
185A ASN 3.4 23.8 - - - +
186A GLY* 4.5 0.4 - - - -
187A LEU* 3.9 28.5 - - + +
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Residues in contact with ILE 143 (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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99A GLY* 4.0 5.1 - - - +
100A LEU* 3.5 42.4 - - - +
101A ALA* 3.5 11.9 - - + +
110A TYR* 3.9 27.4 - - + +
111A TRP* 4.6 2.7 - - - +
112A THR* 4.3 14.8 - - + -
119A ILE* 4.3 22.2 - - + -
142A ALA* 1.3 77.2 - - - +
144A ALA* 1.3 63.7 + - - +
145A LEU* 4.4 13.2 - - + -
152A MET* 4.8 7.6 - - + -
153A TYR 3.2 11.7 - - - +
154A TRP* 4.4 6.1 - - + -
187A LEU* 4.5 2.7 - - - +
272A HIS* 6.0 2.3 - - - -
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Residues in contact with ALA 144 (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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101A ALA* 4.7 1.1 - - - -
143A ILE* 1.3 75.0 - - - +
145A LEU* 1.3 65.2 + - - +
152A MET* 3.4 2.8 - - - -
153A TYR* 2.8 36.6 + - + -
187A LEU* 4.1 31.1 - - + +
188A THR* 4.6 5.2 - - - -
189A LEU* 4.1 21.1 - - + +
191A TYR* 5.8 0.4 - - - +
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Residues in contact with LEU 145 (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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101A ALA* 3.6 23.0 - - + +
102A CYS 3.5 11.9 - - - +
103A ASP* 3.5 34.5 - - + +
104A TRP* 4.2 3.1 - - + -
110A TYR* 3.7 32.1 - - + -
143A ILE* 4.4 4.0 - - + -
144A ALA* 1.3 75.4 - - - +
146A ASP* 1.3 58.2 + - - +
147A PRO* 3.3 16.8 - - + +
151A PHE 3.8 1.8 - - - -
152A MET* 3.7 26.2 - - + -
168A MET* 4.3 9.4 - - + -
189A LEU* 3.2 6.1 - - - +
191A TYR* 2.7 28.5 + - - -
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Residues in contact with ASP 146 (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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145A LEU* 1.3 73.6 - - - +
147A PRO* 1.3 60.9 - - - +
148A SER* 4.3 6.8 + - - -
149A SER* 2.9 30.1 + - - -
150A GLY 2.9 23.6 + - - -
151A PHE* 2.9 18.7 + - + +
153A TYR* 4.3 9.5 + - + -
189A LEU* 3.9 13.4 - - + +
191A TYR* 3.5 23.7 - - - -
194A GLN* 4.8 6.0 + - - +
211A LEU* 4.2 19.8 - - - +
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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