Contacts of the strand formed by residues 205 - 213 (chain A) in PDB entry 6DWZ
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 ARG 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLU* 3.3 17.6 + - - -
196A LEU 3.3 1.0 - - - +
197A HIS* 3.3 26.7 + - - +
198A TYR* 2.8 45.7 + - + +
199A HIS 4.3 0.9 - - - -
200A GLU* 3.6 30.0 - - - +
203A GLU* 2.7 36.0 + - - +
204A LEU* 1.3 72.9 - - - +
206A ASP* 1.3 59.0 + - - +
207A LEU* 4.7 4.0 - - + -
606A ASN* 2.8 36.5 + - + +
607A PHE* 3.2 39.0 - - + +
609A LYS* 5.3 0.2 - - - +
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Residues in contact with ASP 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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195A THR* 4.9 2.6 - - - +
196A LEU 3.5 4.9 - - - -
197A HIS* 3.6 21.3 - - + +
204A LEU* 3.5 4.8 + - + +
205A ARG* 1.3 72.1 - - - +
207A LEU* 1.3 59.8 + - - +
377A CYS* 3.7 36.8 - - + +
570A ALA* 4.0 6.1 - - - +
573A ARG* 3.7 16.4 + - - -
602A SER* 4.0 4.5 + - - -
606A ASN* 2.8 25.1 + - - +
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Residues in contact with LEU 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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162A ILE* 4.8 12.8 - - + -
166A ILE* 4.6 17.7 - - + -
195A THR* 3.0 9.2 - - - -
196A LEU* 2.8 63.6 + - + +
198A TYR* 4.3 16.6 - - + +
205A ARG* 4.7 3.4 - - + -
206A ASP* 1.3 73.8 + - - +
208A ILE* 1.3 69.1 + - - +
209A LEU* 4.6 6.7 - - + -
235A PHE* 6.2 0.9 - - + -
599A PHE* 5.1 9.0 - - + -
602A SER* 3.4 15.0 - - - +
603A PHE* 6.2 1.3 - - + -
606A ASN* 3.0 20.0 - - + +
607A PHE* 5.5 5.6 - - + -
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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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194A VAL 3.6 5.6 - - - +
195A THR* 4.0 7.4 - - + -
207A LEU* 1.3 75.7 - - - +
209A LEU* 1.3 63.6 + - - +
210A GLY* 3.5 27.1 - - - +
211A LEU* 4.4 1.8 - - + +
574A THR* 3.2 43.3 - - + +
577A LEU* 5.4 7.4 - - + -
595A ASP* 5.3 0.4 - - - +
598A LEU* 4.2 21.5 - - + +
599A PHE* 3.2 34.3 - - - +
602A SER* 3.2 32.5 + - - +
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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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159A LYS* 4.7 2.8 - - - +
166A ILE* 5.4 3.6 - - + -
194A VAL* 3.0 23.2 + - + +
196A LEU* 3.5 38.4 - - + +
207A LEU* 3.5 11.5 + - + -
208A ILE* 1.3 75.9 - - - +
210A GLY* 1.3 58.0 + - - +
231A ILE* 3.6 19.1 - - + +
232A PHE* 3.3 39.7 - - + -
234A GLN* 4.7 1.6 + - - -
235A PHE* 3.5 43.8 - - + -
595A ASP* 4.3 3.1 - - - +
599A PHE* 3.6 15.0 - - - +
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Residues in contact with GLY 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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192A LEU 3.6 2.6 - - - +
193A GLY* 3.6 0.5 - - - -
194A VAL* 2.9 31.8 + - - +
208A ILE* 3.5 10.1 - - - +
209A LEU* 1.3 84.8 - - - +
211A LEU* 1.3 60.5 + - - -
212A LYS* 4.0 1.6 - - - -
231A ILE* 3.9 13.8 - - - +
234A GLN* 5.7 1.1 - - - -
574A THR* 6.0 0.3 - - - +
595A ASP* 3.3 11.9 - - - -
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Residues in contact with LEU 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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182A TRP* 4.7 0.4 - - + -
191A PHE* 3.6 48.2 - - + -
192A LEU 3.2 13.9 - - - +
193A GLY* 4.2 2.7 - - - +
208A ILE* 4.4 1.8 - - + +
210A GLY* 1.3 72.7 - - - -
212A LYS* 1.3 60.6 + - - +
574A THR* 5.1 7.4 - - + -
575A PHE* 3.7 27.4 - - + -
578A ALA* 4.1 15.5 - - + -
591A GLN 4.5 3.8 - - - +
594A VAL* 4.3 12.1 - - + -
595A ASP* 3.2 27.7 + - - +
598A LEU* 3.4 34.3 - - + -
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Residues in contact with LYS 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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191A PHE* 3.5 5.1 - - - -
192A LEU* 3.1 31.1 + - - +
210A GLY* 4.0 0.8 - - - -
211A LEU* 1.3 75.2 - - - +
213A SER* 1.3 72.5 + - - +
214A LEU* 3.3 3.1 + - - +
227A LYS* 3.5 34.0 + - + +
230A ALA* 3.2 34.4 - - - +
231A ILE* 4.5 16.7 - - + +
234A GLN* 3.9 17.8 + - - -
591A GLN* 5.7 4.0 - - + +
592A GLN* 5.7 7.9 - - - +
595A ASP* 5.4 5.8 - - + +
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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
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189A ARG* 4.7 4.0 - - - -
190A ASN 3.6 1.1 - - - -
191A PHE* 3.3 27.2 - - - -
212A LYS* 1.3 75.8 - - - +
214A LEU* 1.3 53.6 + - - +
215A ASP* 2.7 22.8 + - - +
227A LYS* 2.4 36.2 + - - -
591A GLN* 3.0 36.2 + - - +
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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