Contacts of the strand formed by residues 191 - 198 (chain A) in PDB entry 4AG1
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 VAL 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A PRO* 3.5 19.7 - - + +
110A PHE 4.0 13.5 - - - +
111A PRO* 3.8 24.0 - - + -
187A LEU* 3.4 5.6 - - - -
188A CYS 3.1 34.0 + - - +
189A ALA* 4.3 8.1 - - + +
190A GLY* 1.3 85.1 - - - +
192A ALA* 1.3 63.5 + - - +
193A GLN* 3.3 19.6 + - - +
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Residues in contact with ALA 192 (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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33A PHE* 4.3 2.5 - - + -
108A LEU* 3.6 29.1 - - + +
109A PRO 3.1 14.2 + - - +
110A PHE* 4.3 16.4 - - + -
111A PRO* 3.4 21.5 - - - +
185A PRO* 5.0 1.1 - - + -
186A LEU 3.7 6.3 - - - +
187A LEU* 4.6 0.7 - - - +
191A VAL* 1.3 68.9 - - - +
193A GLN* 1.3 61.6 + - - +
212A ILE* 3.7 26.3 - - + +
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Residues in contact with GLN 193 (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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111A PRO* 4.0 15.6 - - - +
117A VAL* 3.9 30.8 + - + +
121A ARG* 4.9 3.6 - - - +
166A LEU* 3.6 18.3 - - + +
186A LEU* 2.8 10.4 + - + +
188A CYS* 3.8 31.1 + - + +
191A VAL* 3.3 27.6 + - - +
192A ALA* 1.3 82.6 - - - +
194A GLY* 1.3 58.3 + - - +
211A ARG* 3.9 1.9 - - - +
212A ILE* 3.1 28.1 + - - +
213A SER* 4.6 10.2 + - - -
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Residues in contact with GLY 194 (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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166A LEU* 4.0 7.9 - - - -
185A PRO* 3.4 5.7 - - - +
186A LEU* 2.8 36.6 + - - +
193A GLN* 1.3 80.3 - - - +
195A ILE* 1.3 66.3 + - - +
209A PHE* 4.6 2.0 - - - -
210A THR 3.1 11.0 - - - -
212A ILE* 3.6 10.2 - - - +
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Residues in contact with ILE 195 (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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33A PHE* 3.9 6.3 - - + -
41A LEU* 3.8 20.0 - - + -
42A THR 4.0 11.9 - - - +
43A ALA* 4.2 3.4 - - + +
89A ASP 4.9 1.8 - - - +
90A ILE* 3.7 38.8 - - + -
183A GLY* 3.5 34.8 - - - +
184A GLY 3.3 2.9 - - - -
194A GLY* 1.3 80.1 - - - +
196A VAL* 1.3 72.9 + - - +
209A PHE* 3.1 6.0 - - - -
210A THR* 2.8 39.9 + - - +
212A ILE* 3.8 15.3 - - + -
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Residues in contact with VAL 196 (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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43A ALA* 4.0 4.7 - - - +
125A VAL* 3.5 18.4 - - + -
177A ALA* 3.9 15.5 - - + -
181A ASP* 3.4 22.2 - - + +
182A SER* 3.6 18.8 - - - +
183A GLY 3.0 21.0 + - - -
184A GLY 2.9 21.6 + - - +
195A ILE* 1.3 76.1 - - - +
197A SER* 1.3 59.9 + - - +
208A VAL 5.2 0.2 - - - +
209A PHE* 3.4 30.0 - - + -
16C TRP* 3.9 23.1 - - + -
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Residues in contact with SER 197 (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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45A HIS* 3.0 25.6 - - - -
86A LEU* 4.5 2.4 + - - +
89A ASP* 2.6 32.1 + - - +
165A GLN* 5.3 1.6 + - - -
182A SER* 3.3 8.1 + - - -
195A ILE 3.2 1.2 + - - -
196A VAL* 1.3 75.1 - - - +
198A TYR* 1.3 76.2 + - - +
208A VAL* 3.1 22.6 + - - -
209A PHE 4.6 0.4 - - - -
210A THR* 4.0 18.8 - - - -
16C TRP* 4.0 3.6 + - - -
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Residues in contact with TYR 198 (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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45A HIS* 5.3 0.2 - - + -
85A THR 4.3 8.8 + - - -
86A LEU* 3.5 31.6 - - + -
157A PHE* 3.7 32.7 - + - +
159A ASP* 4.5 14.7 + - - +
160A PHE 4.6 0.3 + - - -
165A GLN* 4.1 7.9 + - - -
197A SER* 1.3 94.2 - - - +
199A GLY* 1.3 70.4 + - - +
207A ALA* 3.6 2.1 - - - +
208A VAL* 2.8 58.3 + - + +
15C ARG* 4.0 22.9 - - + -
16C TRP* 3.6 17.0 - - + -
17C THR* 3.9 21.5 - - + +
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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