Contacts of the strand formed by residues 182 - 186 (chain A) in PDB entry 4GQG
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A MET* 4.9 11.7 - - + -
76A VAL* 6.2 0.2 - - + -
107A VAL* 4.6 4.7 - - + -
109A LEU* 3.7 28.5 - - + -
158A GLY* 3.6 1.2 - - - -
159A VAL* 3.0 27.8 + - - +
180A PRO* 3.5 2.0 - - - +
181A VAL* 1.3 84.1 - - + +
183A ASN* 1.3 62.8 + - - +
184A GLN 4.8 2.0 - - - +
205A ILE* 3.7 5.8 - - - +
206A THR* 2.8 31.5 + - - -
208A THR* 3.0 29.1 + - - +
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Residues in contact with ASN 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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159A VAL* 3.2 25.6 - - + +
161A ASN 3.7 1.6 + - - -
162A PHE 2.9 38.2 + - - -
167A ILE* 3.7 14.4 - - + +
182A THR* 1.3 74.4 + - - +
184A GLN* 1.4 63.6 + - - +
185A VAL* 3.5 17.0 + - - +
196A LEU* 3.8 11.7 - - - +
200A CYS* 4.0 20.2 - - - -
205A ILE* 4.5 1.8 - - + -
206A THR 2.9 8.0 + - - +
207A VAL* 3.3 10.1 - - + +
208A THR 3.1 18.2 + - - -
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 2.8 26.5 + - - -
76A VAL* 4.7 1.6 - - - +
78A LYS* 3.2 9.0 - - - +
109A LEU* 3.5 20.0 - - + +
159A VAL 2.8 13.6 + - - +
160A SER* 2.7 28.1 + - - +
161A ASN 2.9 13.0 + - - -
182A THR* 4.1 1.7 - - + +
183A ASN* 1.4 69.8 + - - +
185A VAL* 1.3 60.5 + - - +
208A THR* 3.2 30.2 - - + +
210A TYR* 3.9 10.2 - - + -
261A ILE* 3.7 14.2 - - - +
401A NAP 2.9 36.8 + - - -
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Residues in contact with VAL 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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161A ASN* 3.7 16.2 - - - +
162A PHE 4.1 2.5 - - - +
183A ASN* 3.5 28.5 - - - +
184A GLN* 1.3 79.7 - - - +
186A GLU* 1.3 67.6 + - - +
187A CYS* 5.0 1.1 - - + -
193A GLN* 3.9 24.0 - - + +
196A LEU* 4.1 17.0 - - + -
207A VAL* 3.9 24.9 - - + -
208A THR 2.9 9.7 + - - +
209A ALA* 3.3 2.3 - - - -
210A TYR* 2.8 30.6 + - - -
297A ARG* 6.2 0.2 - - - +
312A PHE* 6.2 1.8 - - + -
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Residues in contact with GLU 186 (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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161A ASN* 5.0 0.4 + - - -
185A VAL* 1.3 74.9 - - - +
187A CYS* 1.3 64.2 + - - +
188A HIS* 2.8 30.8 + - + +
191A LEU* 3.5 12.1 - - + +
193A GLN* 2.9 27.2 + - - +
210A TYR* 3.4 34.6 - - + +
211A SER* 4.2 4.2 - - - -
297A ARG* 3.5 21.5 + - - +
298A ALA* 2.6 32.6 + - - +
299A CYS* 3.0 30.3 + - - +
312A PHE* 6.4 0.2 - - + -
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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