Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 3DPR
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 THR 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A HIS* 2.9 31.5 + - - -
139A ILE* 1.3 74.0 + - - +
141A MET* 1.3 69.1 + - - +
170A PHE* 5.1 10.8 - - + -
171A TRP 3.5 11.9 - - - +
172A GLN* 3.9 11.0 - - + +
220A ILE* 3.1 5.4 - - - +
221A VAL* 2.5 49.8 + - + -
222A THR* 2.7 12.6 + - - -
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Residues in contact with MET 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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82A LEU* 4.0 11.2 - - + -
127A PRO* 5.8 0.2 - - + -
139A ILE* 5.3 2.2 - - + -
140A THR* 1.3 79.1 - - - +
142A GLN* 1.3 60.7 + - - +
143A TYR* 3.3 34.5 - - + +
170A PHE* 3.4 8.5 - - - +
171A TRP* 2.7 48.0 + - + +
218A SER* 3.5 33.9 - - - +
219A ARG* 3.5 16.4 - - - +
220A ILE* 3.5 26.2 - - - +
221A VAL* 4.0 1.9 - - - +
231A ILE* 4.0 32.1 - - + -
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Residues in contact with GLN 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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141A MET* 1.3 74.6 - - - +
143A TYR* 1.3 69.8 + - - +
144A MET* 4.6 0.4 - - - +
161A TRP* 3.3 48.7 + - + +
163A SER* 4.3 2.0 - - - -
168A SER* 3.6 21.2 + - - -
169A VAL 3.7 3.4 - - - -
170A PHE* 3.0 39.5 - - + -
217A CYS 3.5 0.3 - - - +
218A SER* 3.0 25.5 - - - -
219A ARG* 2.9 40.3 + - + +
221A VAL* 4.1 5.9 - - + +
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Residues in contact with TYR 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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125A LEU* 4.0 22.9 - - + -
127A PRO* 4.4 2.2 - - + +
141A MET* 3.3 43.1 - - + +
142A GLN* 1.3 77.3 - - - +
144A MET* 1.3 61.6 + - - +
145A TYR 3.6 1.9 + - - -
167A ALA 3.8 0.5 - - - +
168A SER* 3.3 4.1 - - - -
169A VAL* 2.8 53.8 + - + +
171A TRP* 4.2 14.6 - - + -
180A PHE* 5.8 0.3 - - - -
216A LEU* 4.3 19.2 - - + +
217A CYS 3.2 5.6 - - - +
218A SER* 3.3 28.3 - - - -
231A ILE* 4.3 0.2 - - - +
233A THR* 2.6 46.5 + - + +
235A ILE* 6.5 0.4 - - + -
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Residues in contact with MET 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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142A GLN* 4.0 1.2 - - - -
143A TYR* 1.3 73.7 - - - +
145A TYR* 1.3 68.9 + - - +
146A VAL* 3.2 24.9 + - + +
151A PRO* 4.4 5.6 - - + +
153A PRO* 4.6 4.7 - - + -
160A ALA* 3.4 42.2 - - + +
161A TRP* 4.3 19.2 - - + -
163A SER* 4.0 6.1 - - - -
166A ASN* 3.1 36.8 - - + +
167A ALA 3.9 0.4 - - - +
168A SER* 3.1 23.6 - - - +
216A LEU* 3.8 2.0 - - - -
217A CYS* 2.7 37.2 + - + +
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Residues in contact with TYR 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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99A ILE* 3.3 33.0 - - + -
143A TYR 3.6 2.8 + - - -
144A MET* 1.3 80.5 - - - +
146A VAL* 1.3 57.6 + - - +
147A PRO* 3.2 39.1 - - + +
148A PRO* 4.3 0.7 - - - +
166A ASN* 3.9 6.4 - - - +
167A ALA* 3.0 29.7 + - + +
180A PHE* 5.7 5.2 - - + -
182A LEU* 5.0 11.0 - - + -
185A LEU* 4.4 19.3 - - + +
213A MET 2.6 23.3 + - - -
215A SER 4.0 1.8 - - - -
216A LEU* 4.0 6.5 - - + +
290A DAO 3.7 23.1 - - + -
24C ALA* 6.2 1.6 - - + -
25C LEU* 5.3 19.0 - - + +
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Residues in contact with VAL 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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144A MET* 3.2 42.0 - - + +
145A TYR* 1.3 76.7 - - - +
147A PRO* 1.3 64.2 - - - +
150A ALA* 3.3 36.1 - - + +
151A PRO 4.0 9.0 - - - +
152A VAL* 4.9 7.4 - - + -
153A PRO* 4.6 3.8 - - + -
166A ASN* 4.6 0.2 - - - +
214A GLY* 3.3 0.2 - - - -
215A SER* 2.6 48.4 + - - +
217A CYS* 4.1 17.7 - - - -
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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