Contacts of the strand formed by residues 203 - 210 (chain A) in PDB entry 5C58
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ARG* 2.8 32.6 + - - +
131A MET* 4.5 9.2 - - + -
142A ILE* 5.0 1.1 - - + -
198A ILE* 3.8 29.6 - - + -
200A SER* 3.6 33.0 - - - +
201A GLU 3.3 2.5 - - - +
202A LEU* 1.3 83.2 - - - +
204A SER* 1.3 59.7 + - - +
205A GLY 4.3 5.6 - - - +
206A VAL* 3.7 24.7 - - + -
228A PHE* 3.8 24.7 - - + -
229A ASN 3.3 22.4 - - - +
230A THR* 4.1 4.0 - - + +
231A VAL* 4.1 5.8 - - - +
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Residues in contact with SER 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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127A SER* 5.2 0.2 - - - -
128A ARG* 3.5 29.5 + - - +
131A MET* 6.0 0.7 - - - -
203A LEU* 1.3 74.7 - - - +
205A GLY* 1.3 58.0 + - - +
229A ASN* 3.0 19.6 + - - +
230A THR 3.6 11.7 + - - -
231A VAL* 4.1 11.1 - - - +
235A ASP* 3.9 24.0 + - - -
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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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125A VAL* 6.2 0.9 - - - -
126A ILE 4.0 9.2 - - - -
127A SER* 5.2 1.6 - - - -
128A ARG 5.0 1.8 - - - -
131A MET* 5.6 2.7 - - - -
203A LEU* 3.5 1.9 - - - -
204A SER* 1.3 85.2 + - - +
206A VAL* 1.3 67.7 + - - +
207A THR* 5.6 0.4 - - - -
229A ASN* 3.0 35.2 + - - +
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Residues in contact with VAL 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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125A VAL* 3.6 4.4 - - - +
126A ILE* 3.1 50.6 + - + +
131A MET* 5.0 4.5 - - - -
142A ILE* 4.7 6.5 - - + -
143A LEU* 5.7 0.9 - - + -
203A LEU* 3.7 17.3 - - + -
205A GLY* 1.3 80.5 - - - +
207A THR* 1.3 66.0 + - - +
208A ILE* 4.1 13.8 + - + +
227A THR 3.3 15.3 - - - +
228A PHE* 3.5 46.4 - - + -
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Residues in contact with THR 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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115A TRP* 4.1 20.0 - - + +
123A VAL* 5.0 3.8 - - - -
124A SER 3.6 4.3 - - - -
125A VAL* 3.8 20.0 - - + -
205A GLY 5.6 0.2 - - - -
206A VAL* 1.3 77.0 - - - +
208A ILE* 1.3 62.6 + - - +
209A ASP* 4.1 2.4 - - - +
225A ILE 3.8 1.4 - - - +
226A ALA* 3.8 0.5 - - - -
227A THR* 2.9 51.2 + - - +
229A ASN* 4.4 13.4 + - - +
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Residues in contact with ILE 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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123A VAL* 3.5 3.3 - - - -
124A SER* 2.8 44.1 + - - +
126A ILE* 5.4 5.2 - - + -
143A LEU* 3.7 31.2 - - + -
146A THR* 4.4 7.9 - - + +
149A ALA* 4.2 17.9 - - + -
162A VAL* 5.3 4.3 - - + -
164A ILE* 4.0 27.8 - - + -
206A VAL* 4.3 16.4 - - + +
207A THR* 1.3 76.6 - - - +
209A ASP* 1.3 60.4 + - - +
210A LYS* 3.7 17.7 + - + +
225A ILE 3.5 2.9 - - - +
226A ALA* 4.5 13.2 - - + -
228A PHE* 5.9 0.4 - - + -
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Residues in contact with ASP 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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121A ARG* 2.9 43.7 + - - +
123A VAL* 3.8 18.8 - - + +
164A ILE* 4.4 0.3 - - - +
207A THR* 4.1 1.9 - - - +
208A ILE* 1.3 71.8 - - - +
210A LYS* 1.3 68.9 + - - +
211A GLY 4.3 0.7 - - - +
213A THR* 4.1 17.0 - - + +
224A GLY* 3.1 5.2 - - - -
225A ILE* 2.8 53.5 + - + +
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Residues in contact with LYS 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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121A ARG* 5.4 2.1 - - - +
122A SER* 3.2 35.4 + - - +
124A SER* 3.8 23.4 - - - -
147A THR* 2.5 51.7 + - - +
148A GLY* 4.6 4.5 - - - -
164A ILE* 4.0 14.6 - - + -
165A ARG* 3.7 17.3 - - - +
208A ILE* 3.7 19.7 + - + +
209A ASP* 1.3 83.1 + - - +
211A GLY* 1.3 63.4 + - - +
212A THR 4.9 1.0 - - - +
213A THR* 4.7 1.9 - - - +
223A GLY 4.0 4.0 - - - -
623A GLU* 4.8 1.7 - - - +
689A GLU* 3.4 24.7 + - - +
691A GLN* 4.0 3.6 + - - +
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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