Contacts of the strand formed by residues 161 - 167 (chain A) in PDB entry 4IRX
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A VAL* 4.2 15.7 - - + -
157A TYR* 3.7 26.9 - - + -
160A GLY* 1.3 76.3 - - - +
162A ARG* 1.3 62.4 + - - +
163A VAL* 4.0 5.5 + - + +
192A ALA 3.0 7.9 + - - +
193A PHE* 3.5 5.3 - - + -
194A LYS* 2.9 26.2 + - - +
225A ASP* 3.5 17.0 - - + +
226A VAL* 5.1 0.2 - - + -
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Residues in contact with ARG 162 (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 ALA* 1.3 73.9 - - - +
163A VAL* 1.3 58.1 + - - +
194A LYS* 3.7 18.8 - - + +
196A VAL* 3.8 22.4 - - + +
219A MSE 3.1 30.1 - - - +
222A THR* 3.0 42.9 + - - +
223A PRO 3.9 6.9 + - - -
224A PRO* 3.7 11.0 - - + +
225A ASP* 2.8 44.3 + - - +
226A VAL 3.2 7.4 + - - -
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Residues in contact with VAL 163 (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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153A VAL* 4.0 26.5 - - + -
161A ALA* 4.2 10.1 - - + +
162A ARG* 1.3 78.0 - - - +
164A VAL* 1.3 73.8 + - - +
165A VAL* 4.1 8.5 - - + -
186A LEU* 4.1 19.7 - - + -
193A PHE* 5.3 1.1 - - + -
194A LYS 2.8 18.2 + - - +
195A ILE* 3.4 4.9 - - - +
196A VAL* 2.9 31.2 + - - +
197A THR 4.0 0.7 + - - +
226A VAL* 3.4 11.7 - - + +
228A LEU* 4.0 27.8 - - + -
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Residues in contact with VAL 164 (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 VAL* 1.3 74.8 - - - +
165A VAL* 1.3 65.5 + - - +
166A ILE* 3.8 28.5 - - + -
196A VAL* 3.6 22.0 - - + -
197A THR* 3.6 7.9 - - + +
212A THR* 6.0 1.6 - - + -
215A ILE* 3.8 24.2 - - + -
219A MSE 3.7 16.4 - - - -
224A PRO* 3.8 15.9 - - + -
226A VAL 2.9 9.8 + - - +
227A ILE* 3.4 13.6 - - + -
228A LEU* 2.8 27.5 + - - +
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Residues in contact with VAL 165 (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 VAL* 4.1 15.5 - - + -
164A VAL* 1.3 78.5 - - - +
166A ILE* 1.3 65.6 + - - +
167A THR* 4.1 15.5 - - + -
179A VAL* 5.0 3.4 - - + -
182A VAL* 4.1 25.6 - - + -
183A HIS* 5.9 0.2 - - - +
195A ILE* 4.1 18.6 - - + -
197A THR 3.0 7.5 + - - +
198A GLU* 3.3 21.2 - - + +
199A GLN 2.9 26.2 + - - +
228A LEU* 3.5 6.3 - - + +
230A LEU* 4.0 24.2 - - + -
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Residues in contact with ILE 166 (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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164A VAL* 3.8 5.6 - - + -
165A VAL* 1.3 75.7 - - - +
167A THR* 1.3 62.3 + - - +
199A GLN* 3.2 6.1 - - + +
201A ALA* 3.8 29.2 - - + +
208A ALA* 5.0 4.0 - - + -
211A VAL* 4.0 10.5 - - + -
212A THR* 4.0 17.3 - - - +
215A ILE* 3.7 29.8 - - + -
227A ILE* 4.0 23.6 - - + -
228A LEU 2.9 11.2 + - - +
229A CYS* 3.5 9.3 - - - -
230A LEU* 2.9 30.0 + - - +
234A MSE 3.8 16.2 - - + +
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Residues in contact with THR 167 (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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165A VAL* 4.1 13.7 - - + -
166A ILE* 1.3 75.0 - - - +
168A ASN* 1.3 61.2 + - - +
170A PRO* 4.8 2.3 - - - +
175A SER* 3.9 12.2 + - - -
179A VAL* 3.6 25.1 - - + -
198A GLU* 4.1 13.9 - - + +
199A GLN 2.8 15.8 + - - +
200A THR* 3.0 40.5 + - - -
201A ALA 3.1 11.4 + - - -
202A ASN 3.7 0.2 + - - -
230A LEU* 4.0 6.5 - - + -
234A MSE 3.2 9.4 - - - +
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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