Contacts of the strand formed by residues 197 - 204 (chain A) in PDB entry 1A3K
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLY 3.2 13.0 - - - +
137A THR* 3.8 13.9 - - + +
195A GLY 4.3 3.1 - - - +
196A LYS* 1.3 95.7 - - + +
198A PHE* 1.3 59.0 + - - +
214A ASN* 4.4 8.3 + - - +
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Residues in contact with PHE 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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134A ILE* 4.1 14.4 - - + -
135A LEU* 3.6 10.7 - - - +
136A GLY* 2.8 62.4 + - - +
137A THR 3.5 11.2 - - - -
138A VAL* 3.8 20.6 - - + -
145A ILE* 5.1 4.7 - - + -
192A PHE* 4.2 21.3 - + + -
196A LYS 4.6 1.1 - - - +
197A PRO* 1.3 75.5 - - - +
199A LYS* 1.3 62.8 + - - +
200A ILE* 3.6 36.1 - - + -
213A VAL* 4.7 2.7 - - + -
214A ASN* 3.3 12.8 - - - +
240A ILE* 3.9 33.4 - - + -
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Residues in contact with LYS 199 (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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133A THR* 4.0 25.8 - - + -
134A ILE 3.3 4.7 - - - +
135A LEU* 3.6 21.5 - - + -
198A PHE* 1.3 74.9 - - - +
200A ILE* 1.3 63.0 + - - +
201A GLN* 4.2 23.1 - - + +
212A ALA 3.9 0.5 - - - +
213A VAL* 3.2 5.4 - - - +
214A ASN* 2.7 41.9 + - - +
215A ASP* 3.3 41.1 + - - +
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Residues in contact with ILE 200 (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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132A ILE 3.7 0.7 - - - +
133A THR* 3.4 3.1 - - - +
134A ILE* 2.8 43.1 + - + +
145A ILE* 5.1 8.1 - - + -
147A LEU* 4.1 24.2 - - + -
159A PHE* 4.2 10.5 - - + -
192A PHE* 3.8 28.3 - - + -
198A PHE* 3.6 30.7 - - + -
199A LYS* 1.3 75.0 - - - +
201A GLN* 1.3 65.6 + - - +
202A VAL* 4.1 16.4 - - + -
211A VAL* 4.1 22.4 - - + -
212A ALA 3.6 4.0 - - - +
213A VAL* 4.3 2.5 - - + +
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Residues in contact with GLN 201 (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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131A LEU* 4.0 25.1 - - + +
132A ILE 3.2 4.5 - - - +
133A THR* 3.9 25.0 + - + +
199A LYS* 4.2 25.2 - - + +
200A ILE* 1.3 80.1 - - - +
202A VAL* 1.3 64.2 + - - +
203A LEU* 4.0 0.7 - - - -
210A LYS 3.6 1.0 - - - +
211A VAL* 3.4 5.5 - - - +
212A ALA* 2.9 48.8 + - + +
215A ASP* 4.0 17.6 + - - +
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Residues in contact with VAL 202 (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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130A MET 3.8 1.4 - - - +
131A LEU* 3.5 3.8 - - - -
132A ILE* 2.9 46.8 + - + +
134A ILE* 5.1 3.4 - - + -
147A LEU* 4.3 11.9 - - + -
149A PHE* 3.8 34.8 - - + -
157A PHE* 4.7 1.1 - - + -
200A ILE* 4.1 17.5 - - + -
201A GLN* 1.3 77.3 - - - +
203A LEU* 1.3 62.6 - - - +
204A VAL* 5.0 0.7 - - + -
209A PHE* 3.9 27.8 - - + -
210A LYS 3.4 7.6 - - - +
211A VAL* 4.3 13.2 - - + -
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Residues in contact with LEU 203 (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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129A ARG* 4.3 3.8 - - - -
130A MET 3.7 14.1 - - - +
131A LEU* 4.1 17.3 - - + -
201A GLN 4.0 1.0 - - - -
202A VAL* 1.3 73.2 - - - +
204A VAL* 1.3 72.3 + - - +
205A GLU* 3.5 26.2 + - + +
209A PHE* 3.7 0.7 - - - -
210A LYS* 2.8 58.5 + - + +
250A ILE* 3.5 38.8 - - + -
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Residues in contact with VAL 204 (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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126A VAL* 4.2 24.9 - - + -
127A VAL 3.4 30.1 - - - +
128A PRO* 3.3 1.1 - - - +
129A ARG* 2.8 29.6 + - - -
130A MET* 2.9 25.2 + - + +
132A ILE* 4.3 13.9 - - + -
202A VAL* 4.9 0.9 - - + +
203A LEU* 1.3 74.9 - - - +
205A GLU* 1.3 72.6 + - - +
208A HIS 4.2 2.0 - - - -
209A PHE* 4.2 21.1 - - + +
223A HIS* 4.6 8.3 - - + +
228A LEU* 4.5 7.4 - - + -
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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