Contacts of the strand formed by residues 181 - 185 (chain A) in PDB entry 4QBT
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 ALA 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.4 8.7 - - + -
37A LYS 3.2 7.4 + - - +
38A ILE* 3.4 19.6 - - + -
39A TYR 3.2 21.8 + - - -
179A VAL* 3.4 13.0 - - - +
180A ASP* 1.3 87.8 - - + +
182A GLN* 1.3 59.9 + - - +
207A ARG* 3.8 4.0 - - - +
208A VAL* 3.1 31.6 - - + +
210A LEU* 5.2 0.7 - - + -
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Residues in contact with GLN 182 (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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38A ILE* 4.4 2.9 - - - -
39A TYR* 3.1 41.6 + - + +
40A TRP* 5.2 0.7 - - - -
41A GLY 5.0 0.5 + - - -
170A GLN* 3.0 30.4 + - - +
174A GLU* 2.9 26.7 + - - +
181A ALA* 1.3 74.8 - - - +
183A PHE* 1.3 65.9 + - - +
192A PHE* 3.4 25.2 - - + -
207A ARG* 4.8 0.4 - - - +
208A VAL 3.1 5.9 + - - +
209A HIS* 3.4 16.1 - - + -
210A LEU* 3.0 24.8 + - - +
506A TYR* 3.2 15.1 - - - -
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Residues in contact with PHE 183 (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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18A LEU* 4.1 8.1 - - + -
38A ILE* 3.9 7.5 - - + +
39A TYR 3.0 12.8 + - - +
40A TRP* 3.2 45.7 - + + -
41A GLY 4.6 0.7 + - - -
55A PRO* 3.9 27.8 - - + -
58A LYS* 3.5 26.0 - - + -
59A ILE* 4.9 0.7 - - + -
62A PHE* 3.6 37.0 - + + -
182A GLN* 1.3 81.1 - - - +
184A GLY* 1.3 73.7 + - - +
210A LEU* 3.2 17.7 - - + +
212A ASN* 3.8 31.6 - - + -
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Residues in contact with GLY 184 (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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40A TRP* 4.2 9.4 - - - -
183A PHE* 1.3 88.3 - - - +
185A GLY* 1.3 63.9 + - - -
188A GLN* 4.5 3.6 - - - -
192A PHE* 3.9 12.8 - - - -
210A LEU 2.9 6.1 + - - +
211A MET* 3.2 5.5 - - - -
212A ASN* 3.0 21.4 + - - -
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Residues in contact with GLY 185 (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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184A GLY* 1.3 76.6 - - - +
186A ILE* 1.3 60.2 + - - -
187A ASP* 3.0 23.1 + - - +
188A GLN* 3.0 21.9 + - - +
211A MET* 3.8 6.5 - - - +
212A ASN* 3.7 11.9 - - - -
213A PRO 5.2 0.4 - - - -
214A MET* 4.3 9.6 - - - -
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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