Contacts of the strand formed by residues 201 - 211 (chain A) in PDB entry 3AJD
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 LEU 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PHE* 4.1 7.7 - - - -
157A PHE 3.6 12.8 - - - +
158A ASP 4.1 2.2 - - - +
159A LYS* 4.2 0.2 - - - -
160A ILE* 3.6 22.7 - - + -
197A GLY 3.2 10.3 + - - +
198A ILE* 3.2 33.9 + - + +
200A LEU* 1.3 79.6 - - - +
202A LYS* 1.3 67.3 + - - +
203A LYS 3.7 0.2 + - - -
205A GLY 3.8 19.1 - - - +
206A GLU 3.5 35.4 - - - +
207A LEU* 4.1 3.8 - - + +
271A LEU 5.1 0.2 - - - +
272A ARG 5.1 0.7 - - - -
273A LYS* 2.9 36.7 + - + +
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Residues in contact with LYS 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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86A PHE* 5.1 4.7 - - - +
156A PHE* 3.7 36.1 - - + -
157A PHE 3.0 17.3 + - - +
158A ASP* 2.9 39.0 + - - +
200A LEU 3.9 0.2 + - - -
201A LEU* 1.3 79.8 - - - +
203A LYS* 1.3 65.7 + - - +
204A ASP 3.3 0.2 + - - -
205A GLY* 2.7 25.1 + - - +
273A LYS* 3.8 2.3 - - - +
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Residues in contact with LYS 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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201A LEU 3.7 1.2 + - - -
202A LYS* 1.3 78.6 - - - +
204A ASP* 1.3 83.4 + - - +
205A GLY 3.3 1.6 + - - -
273A LYS* 4.2 13.5 - - + +
274A ILE* 3.4 35.4 + - - +
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Residues in contact with ASP 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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203A LYS* 1.3 85.8 - - - +
205A GLY* 1.3 65.1 + - - +
206A GLU* 4.1 11.1 - - - +
272A ARG* 4.1 12.9 + - - +
273A LYS 2.8 21.6 + - - +
274A ILE* 5.4 2.3 - - - +
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Residues in contact with GLY 205 (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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157A PHE 4.6 1.3 - - - -
158A ASP* 3.2 18.4 - - - -
201A LEU* 3.8 11.2 - - - -
202A LYS* 2.7 20.2 + - - +
203A LYS 3.1 2.0 + - - -
204A ASP* 1.3 80.8 - - - +
206A GLU* 1.3 59.6 + - - +
272A ARG* 3.3 3.6 - - - -
273A LYS 2.9 25.0 + - - -
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Residues in contact with GLU 206 (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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79A LEU* 3.9 3.2 - - + +
158A ASP 3.1 6.2 + - - +
159A LYS* 3.1 38.8 - - + +
160A ILE 2.9 22.3 + - - +
201A LEU* 3.5 6.4 - - - +
204A ASP 4.1 8.8 - - - +
205A GLY* 1.3 80.4 - - - +
207A LEU* 1.3 61.7 + - - +
236A ILE* 4.0 18.9 - - + +
270A LYS* 3.2 35.5 + - - -
271A LEU 3.2 7.6 - - - +
272A ARG* 4.7 9.8 + - + -
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Residues in contact with LEU 207 (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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160A ILE* 3.2 26.2 - - + +
162A LEU* 4.5 9.4 - - + -
194A ILE* 3.9 30.1 - - + +
197A GLY* 3.7 35.4 - - - +
198A ILE* 4.2 11.4 - - + +
201A LEU* 4.1 12.0 - - + +
206A GLU* 1.3 75.9 - - - +
208A VAL* 1.3 81.6 + - - +
209A TYR* 3.7 5.8 - - + +
270A LYS* 3.3 2.6 - - - +
271A LEU* 2.8 41.3 + - + +
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Residues in contact with VAL 208 (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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75A PRO* 4.1 11.0 - - + +
78A VAL* 3.9 6.1 - - + -
79A LEU* 3.5 42.4 - - + +
160A ILE 2.9 6.7 + - - -
161A LEU* 3.6 21.6 - - + +
162A LEU 2.8 27.2 + - - +
207A LEU* 1.3 79.1 - - - +
209A TYR* 1.3 70.3 + - - +
268A ILE* 4.0 16.4 - - + -
269A ALA 3.3 9.4 - - - +
270A LYS* 3.8 18.4 - - + -
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Residues in contact with TYR 209 (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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162A LEU* 3.3 35.2 - - + -
164A ALA* 4.4 3.1 - - + -
190A GLN* 3.3 37.1 + - + +
194A ILE* 3.8 24.9 - - + -
207A LEU* 3.7 3.6 - - + +
208A VAL* 1.3 73.9 - - - +
210A SER* 1.3 65.6 + - - +
211A THR* 3.8 15.3 - - + +
218A GLU 2.7 29.7 + - - -
222A VAL* 4.1 16.6 - - + -
223A ILE* 4.1 17.0 - - + -
267A PHE* 4.1 25.8 - + - -
268A ILE* 3.4 1.9 - - - -
269A ALA 2.9 33.9 + - - +
271A LEU* 5.6 0.2 - - + -
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Residues in contact with SER 210 (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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75A PRO* 3.4 36.0 - - - +
161A LEU* 4.0 2.1 - - - +
162A LEU 2.9 7.8 + - - +
163A ASP* 2.8 32.4 + - - +
164A ALA* 2.9 25.6 + - - +
208A VAL* 4.5 0.4 - - - -
209A TYR* 1.3 80.4 - - - +
211A THR* 1.3 66.3 + - - +
266A PHE* 4.0 2.0 - - - -
267A PHE 3.1 12.3 - - - -
268A ILE* 4.2 4.5 - - - -
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Residues in contact with THR 211 (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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163A ASP* 4.2 0.4 - - - -
164A ALA* 2.8 27.1 + - - +
165A PRO 4.1 1.9 + - - -
190A GLN* 5.4 1.3 + - - -
209A TYR* 3.8 14.1 - - + +
210A SER* 1.3 79.0 - - - +
212A CYS* 1.3 61.0 + - - +
213A SER* 3.0 23.1 + - - +
218A GLU* 3.5 13.0 - - + +
219A ASN* 3.3 28.7 - - - +
266A PHE* 3.4 9.4 - - - -
267A PHE* 2.9 31.3 + - + -
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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