Contacts of the strand formed by residues 189 - 200 (chain B) in PDB entry 6NQN
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 HIS 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B TYR* 2.7 42.8 + + - -
75B ILE* 3.8 20.9 - - + +
145B LYS* 3.7 1.9 - - - -
146B LEU* 2.9 56.2 + - + +
153B LEU* 4.9 2.0 - - + -
186B PRO* 3.9 24.7 - - + +
187B ASP 2.9 21.4 + - - +
188B TYR* 1.3 79.2 - - - +
190B PHE* 1.3 97.1 + - - +
215B ALA* 4.3 2.0 - - + -
216B HIS 3.5 10.8 - - - +
217B SER* 4.7 2.9 - - - +
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Residues in contact with PHE 190 (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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141A PRO* 3.1 42.2 - - + -
142A SER* 4.2 8.7 - - - -
143A THR* 4.7 2.5 - - - -
143B THR* 4.0 9.2 - - + -
144B GLU 3.2 7.9 - - - +
145B LYS* 3.5 38.4 - - + -
146B LEU* 4.0 0.9 - - - -
188B TYR* 4.0 13.5 - + - -
189B HIS* 1.3 80.9 - - - +
191B VAL* 1.3 65.1 + - - +
192B ASP 4.2 0.4 - - - -
215B ALA* 3.1 7.1 - - - +
216B HIS* 2.8 60.6 + + + +
217B SER* 3.4 22.7 - - - -
218B GLY* 3.4 17.0 - - - -
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Residues in contact with VAL 191 (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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66B ARG* 3.9 15.5 - - - -
69B ALA* 4.4 2.7 - - + -
71B TYR* 3.8 22.0 - - + +
143B THR* 4.4 0.4 - - - -
144B GLU* 2.9 34.2 + - - +
146B LEU* 3.6 19.9 - - + +
189B HIS* 4.4 0.4 - - + -
190B PHE* 1.3 78.8 - - - +
192B ASP* 1.3 70.1 + - - +
193B HIS* 3.3 37.7 - - + +
213B ALA* 4.0 9.0 - - + -
214B GLU 3.4 8.3 - - - +
215B ALA* 3.9 9.9 - - + -
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Residues in contact with ASP 192 (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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216A HIS* 5.4 6.0 - - - -
218A GLY* 5.3 3.7 - - - -
219A LEU* 3.6 35.0 + - + +
142B SER 3.4 5.4 - - - +
143B THR* 2.7 28.0 + - - -
190B PHE 4.2 0.4 - - - -
191B VAL* 1.3 72.6 - - - +
193B HIS* 1.3 59.6 + - - +
213B ALA* 3.1 8.8 - - - +
214B GLU* 2.7 36.7 + - - +
216B HIS* 2.9 34.8 + - - -
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Residues in contact with HIS 193 (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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219A LEU* 4.4 7.2 + - - +
63B KZ4 3.5 31.8 - + + -
66B ARG* 3.5 33.9 - - - -
141B PRO* 3.5 5.4 - - - +
142B SER* 2.9 48.1 + - - +
144B GLU* 3.0 29.1 + - + -
191B VAL* 3.3 36.7 - - + +
192B ASP* 1.3 72.4 - - - +
194B HIS* 1.3 63.9 + - - +
211B GLU* 3.0 22.1 + - - +
212B HIS 3.4 5.2 - - - -
213B ALA* 3.9 1.6 - - + +
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Residues in contact with HIS 194 (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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219A LEU* 4.3 24.3 + - + -
220A PRO 6.0 0.6 - - - -
63B KZ4 5.3 0.7 - - - -
138B LYS* 3.5 26.0 + - - -
139B TRP 4.5 0.4 - - - -
140B GLU 4.8 0.2 - - - -
141B PRO* 4.2 22.8 - - + +
193B HIS* 1.3 76.6 - - - +
195B ILE* 1.3 70.1 + - - +
196B GLU* 3.5 37.2 + - + +
210B HIS 4.1 0.3 - - - +
211B GLU* 3.4 3.9 - - - -
212B HIS* 2.9 40.7 + - + +
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Residues in contact with ILE 195 (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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58B THR* 3.3 44.6 - - - +
59B THR* 3.8 7.0 - - + +
63B KZ4 3.6 42.1 + - + +
138B LYS* 4.6 1.7 - - - +
139B TRP* 3.8 44.5 + - + +
140B GLU 5.5 0.8 + - - -
193B HIS 4.3 0.4 - - - -
194B HIS* 1.3 78.5 - - - +
196B GLU* 1.3 71.3 + - - +
209B LEU* 3.6 11.7 - - + -
210B HIS 3.4 12.1 - - - +
211B GLU* 4.2 5.8 - - + +
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Residues in contact with GLU 196 (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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138B LYS* 4.6 12.9 - - + +
194B HIS* 3.5 38.4 + - + +
195B ILE* 1.3 81.3 - - - +
197B ILE* 1.3 62.6 + - - +
198B LYS* 3.5 30.8 + - + +
209B LEU* 3.5 5.7 - - - +
210B HIS* 2.9 38.0 + - + +
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Residues in contact with ILE 197 (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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54B TYR* 4.1 16.4 - - + -
55B ASP* 3.6 23.8 - - - +
58B THR* 4.0 15.0 - - + -
138B LYS* 6.3 0.6 - - - +
196B GLU* 1.3 71.2 - - - +
198B LYS* 1.3 63.9 + - - +
199B SER 3.6 23.6 - - - +
200B HIS* 4.1 17.9 - - + -
204B TYR* 4.4 14.6 - - + -
207B VAL* 4.1 12.1 - - + -
208B ASN 3.6 5.6 - - - +
209B LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 198 (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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196B GLU* 3.9 32.8 - - + +
197B ILE* 1.3 75.7 - - - +
199B SER* 1.3 64.4 + - - +
208B ASN* 2.9 20.8 + - - +
210B HIS* 3.4 51.9 + - + +
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Residues in contact with SER 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 3.5 3.9 - - - +
198B LYS* 1.3 81.5 - - - +
200B HIS* 1.3 69.6 + - - +
207B VAL* 3.5 1.0 - - - -
208B ASN* 2.8 45.3 + - - +
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Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ILE* 4.1 11.2 - - + -
199B SER* 1.3 81.8 - - - +
201B ASP* 1.3 82.9 + - - +
202B LYS* 4.7 3.8 - - - -
204B TYR* 3.3 56.2 + + + -
206B ASN 3.1 15.0 - - - +
207B VAL* 4.0 4.3 - - + -
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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