Contacts of the strand formed by residues 203 - 213 (chain B) in PDB entry 4D1Q
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 GLU 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B HIS* 3.4 9.8 - - - -
200B GLU* 3.0 43.5 + - - +
201B ASN* 2.8 21.9 + - - +
202B ASN* 1.3 77.8 - - - +
204B LEU* 1.3 64.9 + - - +
205B ARG* 3.7 32.0 + - - +
541B MET* 4.2 6.3 - - - -
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B HIS* 5.8 1.3 - - + -
198B TYR 3.6 4.3 - - - +
199B HIS* 4.3 6.3 - - + -
203B GLU* 1.3 78.2 - - - +
205B ARG* 1.3 67.8 + - - +
206B ASP* 3.8 2.8 + - - +
377B CYS* 3.7 21.4 - - - +
378B SER* 3.7 14.1 + - - +
379B SER* 3.5 35.0 - - - +
380B PRO* 3.7 9.9 - - + -
541B MET* 4.0 18.1 - - - +
559B LEU 5.4 0.4 - - - +
562B LEU* 4.2 4.0 - - + +
563B SER* 3.4 42.2 - - - +
606B ASN* 4.4 3.6 - - - +
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLU* 3.6 17.2 + - - -
196B LEU 4.1 2.2 - - - +
197B HIS* 3.0 33.1 + - - +
198B TYR* 2.7 53.3 + - + +
200B GLU* 3.7 20.4 - - + +
203B GLU* 3.7 34.6 + - - +
204B LEU* 1.3 79.1 - - - +
206B ASP* 1.3 58.7 + - - +
207B LEU* 3.8 5.6 - - + -
377B CYS 5.2 1.0 - - - +
606B ASN* 3.1 32.7 + - - +
607B PHE* 3.6 27.6 - - - -
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B THR* 4.2 4.7 - - - +
197B HIS* 3.7 17.2 - - - -
204B LEU 3.8 2.5 + - - +
205B ARG* 1.3 71.0 - - - +
207B LEU* 1.3 56.8 + - - +
208B ILE* 5.8 0.9 - - - +
377B CYS* 3.6 37.3 - - + +
378B SER* 6.0 0.2 - - - -
570B ALA* 4.2 8.5 - - - +
573B ARG* 4.3 5.0 + - - -
602B SER* 3.8 2.9 + - - -
606B ASN* 2.6 30.5 + - - +
2E G 4.2 15.1 + - - +
3E A 5.3 3.8 + - - -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ILE* 4.3 20.4 - - + -
166B ILE* 4.5 8.1 - - + -
195B THR* 3.1 8.8 - - - -
196B LEU* 2.6 50.8 + - + +
197B HIS* 4.5 0.8 + - - -
198B TYR* 5.5 5.2 - - + +
205B ARG* 4.9 5.2 - - + -
206B ASP* 1.3 78.1 + - - +
208B ILE* 1.3 67.5 + - - +
209B LEU* 3.5 21.0 + - + -
599B PHE* 5.1 3.6 - - + -
602B SER* 3.1 33.0 - - - +
603B PHE* 4.2 6.1 - - + +
606B ASN* 3.2 25.4 - - + +
607B PHE* 4.7 9.4 - - + -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B VAL 3.7 6.3 - - - +
195B THR* 4.2 7.4 - - + -
206B ASP* 5.8 0.9 - - - +
207B LEU* 1.3 77.5 - - - +
209B LEU* 1.3 60.9 + - - +
210B GLY* 3.6 21.5 - - - +
574B THR* 3.9 37.9 - - + +
577B LEU* 4.2 22.4 - - + -
598B LEU* 4.6 33.2 - - + +
599B PHE* 3.5 20.1 - - - +
602B SER* 2.9 23.8 + - - +
605B LYS* 6.0 1.8 - - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 4.3 2.3 - - - +
166B ILE* 4.2 8.3 - - + -
194B VAL* 2.7 29.0 + - + +
196B LEU* 3.9 24.0 - - + -
207B LEU* 3.5 22.2 + - + -
208B ILE* 1.3 74.8 - - - +
210B GLY* 1.3 56.3 + - - +
231B ILE* 3.9 14.6 - - + +
232B PHE* 3.4 42.8 - - + -
234B GLN* 4.1 5.9 - - - +
235B PHE* 3.6 46.5 - - + -
595B ASP* 4.2 2.3 - - - +
599B PHE* 4.2 8.0 - - + -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU 3.5 1.6 - - - +
193B GLY* 3.4 3.1 - - - -
194B VAL 2.9 27.4 + - - +
208B ILE* 3.5 13.4 - - - +
209B LEU* 1.3 83.8 - - - +
211B LEU* 1.3 60.8 + - - +
212B LYS 4.0 1.3 - - - -
231B ILE* 4.2 12.9 - - - +
574B THR* 5.2 0.7 - - - +
595B ASP* 3.2 15.0 - - - -
598B LEU* 6.3 0.2 - - - -
599B PHE* 5.9 0.7 - - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B TRP* 4.6 5.2 - - + -
191B PHE* 3.1 51.9 - - + -
192B LEU 3.4 14.4 - - - +
193B GLY* 4.0 4.5 - - - +
210B GLY* 1.3 72.9 - - - +
212B LYS* 1.3 60.5 + - - +
574B THR* 4.4 12.1 - - + -
575B PHE* 4.3 9.0 - - + -
578B ALA* 3.8 19.1 - - + -
591B GLN* 4.8 3.3 - - - +
594B VAL* 4.0 11.0 - - + -
595B ASP* 3.1 26.6 + - - +
598B LEU* 3.4 35.0 - - + -
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 5.5 0.8 - - - +
191B PHE* 3.5 2.4 - - - -
192B LEU* 2.8 34.0 + - - +
210B GLY 4.0 0.2 - - - -
211B LEU* 1.3 76.4 - - - +
213B SER* 1.3 62.7 + - - +
227B LYS* 3.6 32.3 - - + -
230B ALA 6.4 0.2 - - - -
231B ILE* 4.0 23.8 - - + +
234B GLN* 3.3 38.7 - - - +
591B GLN* 5.7 4.0 - - + +
592B GLN* 5.0 17.2 + - - +
595B ASP* 3.2 34.7 + - - +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ARG* 5.0 8.3 - - - -
190B ASN 3.6 9.9 - - - -
191B PHE* 3.8 12.2 - - - -
212B LYS* 1.3 74.5 - - - +
214B LEU* 1.3 61.0 + - - +
215B ASP* 2.8 21.9 + - - -
216B PHE* 6.5 0.2 - - - -
227B LYS* 3.0 26.0 + - - -
591B GLN* 3.2 39.0 + - - +
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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