Contacts of the strand formed by residues 210 - 221 (chain D) in PDB entry 6B0B
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 ILE 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D LYS* 6.5 0.9 - - + -
46D LEU 3.8 5.4 - - - +
47D LYS* 3.7 37.2 - - + +
48D VAL 5.2 0.2 - - - +
203D SER* 3.9 0.9 + - - +
204D HIS* 3.2 24.4 + - - -
205D ASN* 3.3 20.1 + - + +
209D THR* 1.3 89.0 - - - +
211D VAL* 1.3 63.4 + - - +
212D GLU* 5.7 5.6 - - + -
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Residues in contact with VAL 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 3.6 1.4 - - - -
46D LEU* 2.9 36.9 + - - +
58D TRP* 3.4 49.4 - - + +
201D ILE* 4.0 10.5 - - + -
203D SER 3.4 7.4 - - - +
204D HIS* 4.1 10.8 - - + -
208D TYR* 3.9 29.4 - - + +
209D THR 4.2 0.4 - - - -
210D ILE* 1.3 79.3 - - - +
212D GLU* 1.3 68.5 + - - +
213D GLN* 4.0 14.6 - - + -
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Residues in contact with GLU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A TYR* 2.3 33.0 + - + -
43D THR* 6.1 2.1 - - - -
44D ALA 3.1 5.4 - - - +
45D LYS* 3.4 43.2 - - + +
201D ILE* 3.7 3.8 - - - -
202D THR* 2.9 37.7 + - - +
203D SER* 3.0 24.9 + - - +
210D ILE* 5.7 6.5 - - + -
211D VAL* 1.3 77.3 - - - +
213D GLN* 1.3 63.3 + - - +
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Residues in contact with GLN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D GLN 3.8 0.2 - - - +
43D THR* 3.0 9.4 - - - -
44D ALA* 2.9 37.3 + - + +
46D LEU* 4.2 10.9 - - + +
58D TRP* 2.7 32.7 + - - -
62D SER* 3.8 22.2 + - - +
65D PHE* 3.3 32.1 - - - +
199D LEU* 4.2 9.5 - - + +
200D ASP 3.4 7.4 - - - +
201D ILE* 3.7 18.4 - - + -
202D THR* 4.2 2.9 - - - -
211D VAL* 4.0 6.5 - - + -
212D GLU* 1.3 77.6 - - - +
214D TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TRP* 4.6 9.3 + - - -
151A HIS* 5.1 10.4 + + - -
159A PRO* 4.2 22.8 + - + -
160A TYR* 4.2 11.4 - - + -
162A MET* 6.1 2.7 - - - -
163A LEU* 5.8 3.8 - - + -
41D THR* 3.7 18.8 - - + +
42D GLN 3.2 14.8 - - - -
43D THR* 3.9 14.6 - - + -
198D LYS* 5.1 1.8 - - + -
199D LEU* 3.4 6.2 - - - +
200D ASP* 2.9 58.3 + - + +
202D THR* 3.6 20.0 - - + -
213D GLN* 1.3 75.6 - - - +
215D GLU* 1.3 77.3 + - - +
216D ARG* 3.7 33.9 + - + +
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Residues in contact with GLU 215 (chain D).
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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40D GLY 3.3 0.9 - - - +
41D THR* 3.2 6.6 - - - -
42D GLN* 2.9 64.4 + - + +
62D SER 5.2 0.2 - - - +
65D PHE* 3.9 23.1 - - - +
70D LYS* 4.8 16.2 + - - +
72D TYR* 4.9 4.5 - - - +
73D VAL* 5.0 2.3 - - - +
197D ILE* 4.4 14.9 - - + +
198D LYS 3.6 6.7 - - - +
199D LEU* 4.0 20.2 - - + +
214D TYR* 1.3 82.3 - - - +
216D ARG* 1.3 71.1 + - - +
217D ALA* 4.4 11.8 - - + +
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Residues in contact with ARG 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ALA* 3.3 40.7 + - - +
143A ASP* 5.7 1.4 + - - -
145A TRP* 3.9 17.5 - - - -
146A GLU* 3.5 27.7 + - + +
151A HIS* 6.0 6.1 - - + +
39D GLU 4.3 7.0 + - - -
40D GLY 3.0 18.6 - - - -
41D THR* 3.4 17.8 - - - +
74D LYS* 6.3 1.0 - - - +
196D ASN 4.0 1.3 - - - +
197D ILE* 3.3 4.7 - - - +
198D LYS* 2.9 44.7 + - + +
214D TYR* 3.7 19.7 + - + +
215D GLU* 1.3 74.1 - - - +
217D ALA* 1.3 69.4 + - - +
218D GLU* 4.5 14.8 + - + +
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D GLY* 3.1 10.9 + - - -
72D TYR 4.2 3.6 + - - +
73D VAL* 3.8 34.8 - - + -
74D LYS* 3.0 27.8 + - - +
196D ASN 3.3 5.8 - - - -
197D ILE* 3.9 17.3 - - + -
215D GLU* 4.4 9.6 - - - +
216D ARG* 1.3 80.3 - - - +
218D GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 218 (chain D).
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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146A GLU* 5.0 7.8 - - - +
74D LYS* 3.8 37.5 + - + +
76D PRO* 6.2 1.3 - - + -
195D VAL* 3.9 4.8 - - - +
196D ASN* 2.9 38.7 + - + +
216D ARG* 4.5 17.9 + - + +
217D ALA* 1.3 75.2 - - - +
219D GLY* 1.3 72.8 + - - +
220D ARG* 4.1 22.0 + - - +
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Residues in contact with GLY 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.6 1.5 - - - +
74D LYS 3.3 16.0 + - - -
75D HIS* 5.9 4.0 - - - -
76D PRO* 4.5 19.9 - - - +
79D ILE* 5.6 2.9 - - - -
193D TYR* 5.0 5.8 - - - -
194D ASN 3.7 5.4 - - - -
195D VAL* 4.1 14.0 - - - +
218D GLU* 1.3 81.7 - - - +
220D ARG* 1.3 65.8 + - - +
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Residues in contact with ARG 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLU* 5.1 7.7 + - - -
79D ILE* 5.5 1.5 - - - +
193D TYR* 3.3 8.7 - - - +
194D ASN* 2.8 45.7 + - - +
196D ASN* 3.3 35.6 - - - +
218D GLU* 4.4 23.3 + - - +
219D GLY* 1.3 79.8 + - - +
221D HIS* 1.3 68.1 + - - +
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Residues in contact with HIS 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO* 5.6 0.6 - - - +
78D ASP* 5.2 9.5 + - - -
79D ILE* 3.4 36.7 - - + +
192D ALA 4.7 3.4 - - - +
193D TYR* 4.7 2.7 - - + +
194D ASN* 3.2 8.8 + - - +
220D ARG* 1.3 78.7 - - - +
222D SER* 1.3 67.6 + - - +
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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