Contacts of the strand formed by residues 201 - 207 (chain A) in PDB entry 4IE6
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 4.1 21.5 - - + -
99A ILE 3.5 9.6 - - - +
100A GLY* 4.1 1.3 - - - -
104A CYS* 4.0 16.2 - - - -
106A TYR* 4.8 5.6 - - + -
115A THR* 3.9 22.7 - - + -
118A TRP* 4.1 6.2 - - - -
143A ASN* 4.4 0.2 - - - +
199A TYR* 3.5 3.0 - - - +
200A ASN* 1.3 103.2 + - - +
202A THR* 1.3 60.9 + - - +
321A HIS* 3.4 4.5 - - - +
322A ARG* 3.0 43.1 + - + +
324A ALA* 4.2 13.5 - - + -
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Residues in contact with THR 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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97A ILE 3.9 0.5 - - - +
98A LEU* 3.6 6.6 - - - +
99A ILE* 2.9 46.8 + - + +
118A TRP* 3.8 16.1 - - + -
139A PHE* 4.4 5.6 - - + -
201A VAL* 1.3 75.0 - - - +
203A LEU* 1.3 62.1 + - - +
204A LEU* 3.4 18.7 - - + +
319A SER* 2.8 24.9 + - - +
320A THR 3.3 17.3 + - - -
321A HIS* 3.8 17.0 - - + -
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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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96A ARG* 4.0 31.2 - - + +
97A ILE 3.6 16.2 - - - +
98A LEU* 3.8 13.0 - - + -
106A TYR* 4.0 26.5 - - + -
108A TYR* 5.0 5.6 - - + -
113A LEU* 3.3 31.4 - - + -
202A THR* 1.3 74.1 + - - +
204A LEU* 1.3 61.6 + - - +
205A ASN* 3.2 11.4 + - - +
320A THR* 3.0 40.5 + - - +
322A ARG* 4.2 17.9 - - - +
602A UN9 5.1 5.6 - - + -
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Residues in contact with LEU 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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69A PHE* 4.0 19.5 - - + -
72A LEU* 3.6 20.2 - - + -
78A LEU* 4.2 8.1 - - + -
96A ARG* 3.0 29.8 - - - +
97A ILE* 3.0 25.7 + - + +
99A ILE* 3.5 26.9 - - + -
139A PHE* 3.7 15.5 - - + -
202A THR* 3.4 38.1 - - + +
203A LEU* 1.3 72.6 - - - +
205A ASN* 1.3 60.7 + - - +
317A PHE* 6.3 0.7 - - + -
318A SER 3.2 4.5 - - - +
319A SER* 3.6 10.3 - - - +
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Residues in contact with ASN 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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69A PHE* 5.5 0.2 - - - -
78A LEU* 4.7 2.5 - - - -
94A VAL* 3.5 13.9 - - + -
95A SER 3.1 5.4 - - - -
96A ARG* 2.5 40.2 + - - +
203A LEU* 3.2 20.5 + - - +
204A LEU* 1.3 74.3 - - - +
206A PHE* 1.3 61.4 - - - +
316A ARG* 4.5 2.2 - - - +
317A PHE* 3.1 9.2 - - - +
318A SER* 2.9 52.4 + - - +
320A THR* 3.6 12.9 + - - +
602A UN9 3.7 12.9 + - - +
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Residues in contact with PHE 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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73A HIS* 3.3 32.5 - + - -
78A LEU* 4.5 8.5 - - + -
93A PRO 4.7 0.3 - - - +
94A VAL* 3.7 3.9 - - - -
95A SER* 2.8 46.7 + - - +
205A ASN* 1.3 75.8 - - - +
207A MET* 1.3 68.4 + - - +
208A ASP* 3.9 31.6 - - + -
249A CYS* 5.3 0.4 - - - -
315A PRO* 3.8 22.7 - - + -
316A ARG 3.5 8.3 - - - -
317A PHE* 3.4 46.2 - + + -
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Residues in contact with MET 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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93A PRO* 3.9 25.6 - - - +
94A VAL* 4.5 9.6 - - + -
206A PHE* 1.3 80.2 - - - +
208A ASP* 1.3 66.1 + - - +
209A PRO* 3.7 24.2 - - + +
212A MET* 4.0 12.8 - - + -
215A LEU* 3.6 44.9 - - + -
227A ALA* 4.2 13.7 - - + -
270A TRP* 3.8 29.6 - - + -
311A ALA* 4.2 0.2 - - + -
315A PRO* 3.2 2.8 - - - +
316A ARG 3.0 34.0 + - - +
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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