Contacts of the strand formed by residues 189 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A TYR* 2.7 41.3 + + - -
75A ILE* 3.8 18.5 - - + +
78A TYR* 6.2 0.2 - - + -
145A LYS* 3.7 2.3 - - - -
146A LEU* 2.8 55.7 + - + +
153A LEU* 4.6 2.7 - - + -
186A PRO* 3.7 29.3 - - + +
187A ASP 2.8 19.3 + - - +
188A TYR* 1.3 77.5 - - - +
190A PHE* 1.3 98.7 + - - +
191A VAL* 4.4 0.9 - - + -
215A ALA* 4.4 1.1 - - + -
216A HIS 3.6 9.0 - - - +
217A SER* 5.0 2.7 - - - +
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Residues in contact with PHE 190 (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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143A THR* 4.0 8.7 - - + -
144A GLU 3.1 8.1 - - - +
145A LYS* 3.6 45.1 - - + -
146A LEU* 4.1 0.4 - - - -
188A TYR* 3.9 13.9 - + - -
189A HIS* 1.3 83.7 - - - +
191A VAL* 1.3 66.4 + - - +
192A ASP 4.2 0.2 - - - -
215A ALA* 3.1 7.4 - - - +
216A HIS* 3.0 50.9 + + + +
217A SER* 3.5 9.0 - - - -
218A GLY* 3.4 33.4 - - - -
141B PRO* 3.0 41.3 - - + -
142B SER* 4.2 4.7 - - - -
143B THR* 4.7 1.3 - - - -
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Residues in contact with VAL 191 (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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66A ARG* 3.9 15.7 - - + -
69A ALA* 4.4 2.7 - - + -
71A TYR* 3.9 21.8 - - + +
143A THR* 4.4 0.2 - - - -
144A GLU* 2.9 32.9 + - - +
146A LEU* 3.7 20.6 - - + +
189A HIS* 4.4 0.4 - - + -
190A PHE* 1.3 78.5 - - - +
192A ASP* 1.3 68.7 + - - +
193A HIS* 3.3 38.8 - - + +
213A ALA* 4.0 9.2 - - + -
214A GLU 3.4 8.1 - - - +
215A ALA* 4.0 9.4 - - + -
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Residues in contact with ASP 192 (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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142A SER 3.3 5.6 - - - +
143A THR* 2.6 28.8 + - - +
191A VAL* 1.3 72.0 - - - +
193A HIS* 1.3 59.7 + - - +
213A ALA* 3.1 8.7 - - - +
214A GLU* 2.8 36.1 + - + +
216A HIS* 2.8 33.3 + - - -
216B HIS* 5.1 9.6 - - - -
218B GLY* 5.4 1.6 - - - -
219B LEU* 3.7 31.0 + - + +
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Residues in contact with HIS 193 (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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63A KZ4 3.4 31.7 - + + -
66A ARG* 3.5 32.8 - - - -
141A PRO* 3.3 5.9 - - - +
142A SER* 2.8 51.5 + - - +
144A GLU* 2.9 29.0 + - + -
191A VAL* 3.3 36.1 - - + +
192A ASP* 1.3 72.8 - - - +
194A HIS* 1.3 64.4 + - - +
211A GLU* 2.8 23.8 + - - +
212A HIS 3.5 4.7 - - - -
213A ALA* 3.8 2.6 - - + +
219B LEU* 4.1 6.0 + - - +
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Residues in contact with HIS 194 (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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63A KZ4 5.3 0.4 - - - -
138A LYS* 3.0 27.8 + - - -
139A TRP 4.5 1.1 - - - -
140A GLU 4.8 0.2 - - - -
141A PRO* 3.9 25.4 - - + +
193A HIS* 1.3 75.5 - - - +
195A ILE* 1.3 71.2 + - - +
196A GLU* 3.8 16.2 - - + +
210A HIS 4.1 0.2 - - - +
211A GLU* 3.4 3.6 - - - -
212A HIS* 2.9 37.8 + - + +
219B LEU* 3.1 31.9 + - + -
220B PRO 3.4 11.5 + - - +
221B ARG* 3.4 33.6 - - + -
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Residues in contact with ILE 195 (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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58A THR* 3.4 44.0 - - - +
59A THR* 3.8 7.2 - - + +
63A KZ4 3.7 40.7 + - + +
138A LYS* 4.5 2.6 + - - +
139A TRP* 3.8 44.7 + - + +
140A GLU 5.5 0.8 + - - +
194A HIS* 1.3 78.9 - - - +
196A GLU* 1.3 70.2 + - - +
209A LEU* 3.8 11.4 - - + -
210A HIS 3.3 12.3 - - - +
211A GLU* 4.0 6.5 - - + -
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Residues in contact with GLU 196 (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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138A LYS* 4.5 10.8 - - - +
194A HIS* 3.8 25.4 - - + +
195A ILE* 1.3 81.6 - - - +
197A ILE* 1.3 62.5 + - - +
198A LYS* 3.4 33.3 + - + +
209A LEU* 3.5 6.2 - - - +
210A HIS* 2.8 44.8 + - + +
212A HIS* 6.1 0.5 - - - +
220B PRO 5.0 0.9 - - - +
221B ARG* 3.0 48.0 + - - +
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Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A TYR* 4.3 11.2 - - + -
55A ASP* 3.6 25.1 - - - +
58A THR* 4.1 13.2 - - + -
137A VAL 6.0 0.4 - - - +
138A LYS* 6.1 2.0 - - - +
196A GLU* 1.3 73.0 - - - +
198A LYS* 1.3 61.5 + - - +
199A SER 3.5 24.0 - - - +
200A HIS* 3.9 20.2 - - + -
204A TYR* 4.2 19.7 - - + -
207A VAL* 3.9 11.4 - - + -
208A ASN 3.6 5.6 - - - +
209A LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 198 (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 GLU* 4.0 37.1 + - + +
197A ILE* 1.3 75.2 - - - +
199A SER* 1.3 63.5 + - - +
208A ASN* 2.9 22.0 + - - +
210A HIS* 3.3 43.4 + - + +
221B ARG 5.9 2.4 - - - -
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Residues in contact with SER 199 (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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197A ILE* 3.5 8.4 - - - +
198A LYS* 1.3 80.6 - - - +
200A HIS* 1.3 68.3 + - - +
207A VAL* 3.5 0.2 - - - -
208A ASN* 2.9 43.0 + - - +
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Residues in contact with HIS 200 (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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197A ILE* 3.9 14.6 - - + -
199A SER* 1.3 79.3 - - - +
201A ASP* 1.3 81.9 + - - +
202A LYS* 5.0 4.0 - - - -
204A TYR* 3.3 52.8 + + + -
206A ASN* 3.2 15.3 - - - +
207A VAL* 4.0 4.0 - - + -
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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