Contacts of the strand formed by residues 207 - 215 (chain A) in PDB entry 5J3S
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 ASN 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLY* 3.0 30.1 + - - +
174A HIS* 4.8 5.5 - - - +
179A PHE* 5.7 2.1 - - - +
180A THR* 4.2 16.8 + - - +
196A ILE* 3.3 18.8 - - + +
197A ILE 3.7 3.1 - - - +
198A PRO* 3.5 24.9 - - + +
199A PHE* 4.0 3.1 - - - +
205A MET 5.4 1.4 + - - +
206A ARG* 1.3 79.9 - - - +
208A LEU* 1.3 66.7 + - - +
209A LEU* 4.2 1.0 + - - +
225A SER* 3.2 21.5 + - - -
226A HIS 4.4 2.1 + - - -
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Residues in contact with LEU 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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196A ILE* 3.6 3.4 - - - +
197A ILE* 2.8 56.0 + - + +
198A PRO 5.7 1.8 - - - +
199A PHE* 5.2 11.9 - - + +
207A ASN* 1.3 77.7 - - - +
209A LEU* 1.3 60.1 + - - +
210A CYS* 3.9 2.2 + - - +
223A MET* 6.5 0.7 - - + -
224A THR 3.8 5.4 - - - +
225A SER* 3.2 25.6 - - - +
227A LEU* 5.2 2.2 - - + -
240A GLN* 5.1 7.9 - - + +
243A MET* 4.3 24.5 - - + +
244A VAL* 3.9 28.0 - - + -
247A LYS* 5.5 5.4 - - + -
259A PHE* 6.3 0.4 - - + -
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Residues in contact with LEU 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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171A ILE* 3.3 46.0 - - + +
172A THR 4.2 1.8 - - - +
173A GLY* 4.0 11.0 - - - +
180A THR* 3.9 20.4 - - - +
181A ALA* 4.0 7.6 - - - -
182A ILE* 3.6 25.7 - - + +
195A GLU 3.7 14.1 - - - +
196A ILE* 3.8 17.3 - - + +
207A ASN* 4.2 1.5 + - - +
208A LEU* 1.3 72.2 - - - +
210A CYS* 1.3 63.5 + - - +
211A VAL* 4.6 0.4 - - + -
223A MET* 3.3 3.5 - - - +
224A THR* 2.8 46.2 + - + +
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Residues in contact with CYS 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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195A GLU* 2.9 51.4 + - + +
208A LEU* 3.9 2.8 + - + +
209A LEU* 1.3 75.2 - - - +
211A VAL* 1.3 72.6 + - - +
212A HIS* 3.4 34.5 - - - -
221A CYS* 4.5 2.2 - - - -
222A LEU 3.2 9.9 - - - +
223A MET* 3.9 27.6 - - + +
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Residues in contact with VAL 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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171A ILE* 4.2 24.5 - - + -
182A ILE* 3.9 22.2 - - + -
184A LEU* 3.7 16.2 - - + -
191A LEU* 5.2 3.8 - - + -
193A SER 3.2 16.4 - - - +
194A GLN* 4.1 14.8 - - + +
209A LEU* 4.6 1.1 - - + -
210A CYS* 1.3 80.9 - - - +
212A HIS* 1.3 65.0 + - - +
213A VAL* 3.5 24.8 + - + +
222A LEU* 2.7 38.9 + - + +
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Residues in contact with HIS 212 (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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192A LYS* 2.9 14.1 + - + +
193A SER* 2.9 58.0 + - - +
195A GLU* 2.9 22.4 + - + -
210A CYS* 3.4 21.7 - - - -
211A VAL* 1.3 69.2 - - - +
213A VAL* 1.3 62.5 + - - +
221A CYS* 3.2 26.6 - - + +
223A MET* 5.8 0.4 - - + -
251A ALA* 4.6 13.7 - - + -
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Residues in contact with VAL 213 (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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184A LEU* 3.7 17.9 - - + -
189A VAL* 3.6 18.6 - - + -
190A LYS 3.3 14.4 - - - +
191A LEU* 4.8 0.2 - - - -
192A LYS* 4.3 5.5 - - - +
211A VAL* 3.5 22.4 + - + +
212A HIS* 1.3 79.0 - - - +
214A ASN* 1.3 64.9 + - - +
215A VAL* 4.1 11.2 - - + -
218A ASN 4.2 3.9 - - - +
219A GLU* 4.7 3.5 - - - -
220A LEU 3.4 29.4 + - - +
222A LEU* 3.7 27.1 - - + -
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Residues in contact with ASN 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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188A ARG 4.2 2.3 - - - +
190A LYS* 3.1 35.7 + - + +
192A LYS* 5.6 4.7 - - + -
213A VAL* 1.3 79.5 - - - +
215A VAL* 1.3 60.5 + - - +
216A SER 4.2 1.5 + - - +
217A GLY* 3.2 32.4 - - - +
218A ASN 3.1 20.1 - - - +
219A GLU* 4.9 1.4 - - - +
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Residues in contact with VAL 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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113A MET 5.2 6.7 - - - +
114A PHE* 4.7 26.5 - - + -
146A ASP* 5.8 1.3 - - + -
147A VAL* 5.7 0.2 - - + -
188A ARG* 4.0 23.6 - - + +
189A VAL* 3.6 36.3 - - + -
213A VAL* 4.1 11.6 - - + +
214A ASN* 1.3 74.6 - - - +
216A SER* 1.3 77.0 + - - +
217A GLY 3.1 0.9 - - - -
218A ASN* 3.0 29.0 + - + +
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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