Contacts of the strand formed by residues 212 - 217 (chain A) in PDB entry 4ECX
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 CYS 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.7 17.7 - - + -
13A ASP 3.3 16.2 - - - +
14A MET* 3.7 17.0 - - - -
15A ASP* 3.6 7.6 - - - -
201A ARG* 3.0 60.1 + - - +
204A ILE* 4.3 16.4 - - - -
210A PHE 5.5 0.2 - - - -
211A GLN* 1.3 77.6 - - - +
213A SER* 1.3 64.0 + - - +
233A ASN* 3.5 6.9 + - - -
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 3.6 4.2 - - - +
13A ASP 2.9 29.9 + - - -
15A ASP* 2.9 17.2 + - - -
201A ARG* 4.4 2.0 - - - -
212A CYS* 1.3 74.0 - - - +
214A ALA* 1.3 65.2 + - - +
227A CYS* 3.7 8.5 - - - -
230A ASN 4.2 0.7 - - - -
231A LYS* 3.3 34.3 - - - +
232A PRO 3.6 1.2 - - - -
233A ASN 3.2 15.6 + - - -
234A ARG 3.1 14.9 + - - -
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Residues in contact with ALA 214 (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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10A ALA* 5.5 0.2 - - + -
11A LEU 3.1 13.0 - - - +
12A VAL* 4.0 8.1 - - + -
197A VAL* 3.6 31.4 - - + -
201A ARG* 3.8 9.0 - - - -
213A SER* 1.3 80.2 - - - +
215A GLY* 1.3 62.1 + - - +
227A CYS* 3.6 11.1 - - - +
234A ARG 3.2 5.7 + - - +
235A GLN* 3.1 7.8 - - + +
236A THR 3.0 23.9 + - - -
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Residues in contact with GLY 215 (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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10A ALA* 3.0 8.3 - - - +
11A LEU 2.9 32.4 + - - -
214A ALA* 1.3 75.5 - - - +
216A ILE* 1.3 62.2 + - - +
223A ALA* 3.3 23.9 - - - +
226A ALA* 3.7 1.1 - - - -
227A CYS* 3.4 10.6 - - - +
236A THR 3.4 7.4 - - - -
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Residues in contact with ILE 216 (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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8A VAL* 4.1 20.6 - - + -
9A VAL 3.6 4.9 - - - +
10A ALA* 4.3 1.8 - - + -
121A LEU* 5.3 0.2 - - + -
145A THR* 5.8 0.2 - - + -
190A LEU* 3.7 28.0 - - + +
193A GLY 4.3 1.1 - - - -
194A ALA* 4.2 13.2 - - + +
197A VAL* 3.8 26.9 - - + -
215A GLY* 1.3 81.2 - - - +
217A SER* 1.3 63.0 + - - +
223A ALA* 4.8 0.2 - - - -
226A ALA* 4.2 1.0 - - - +
235A GLN* 3.7 40.2 - - + +
236A THR 3.0 17.8 + - - +
237A LEU* 3.5 9.2 - - + +
238A VAL* 3.0 25.8 + - - +
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.6 0.7 - - - +
9A VAL 2.8 30.5 + - - -
190A LEU* 3.4 19.5 - - - +
215A GLY 4.2 0.2 - - - -
216A ILE* 1.3 76.8 - - - +
218A HIS* 1.3 67.3 + - - +
219A ASN 3.4 1.8 - - - -
222A LEU* 3.3 41.2 - - - +
223A ALA* 3.9 10.2 - - - +
238A VAL* 2.7 24.7 + - - -
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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