Contacts of the strand formed by residues 214 - 224 (chain B) in PDB entry 1QQW
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 GLY 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B PHE* 4.1 2.7 - - - -
148B ASN 3.5 8.1 - - - -
213B ASN* 1.3 78.6 - - - +
215B TYR* 1.3 67.2 + - - -
235B HIS* 3.3 2.9 - - - -
236B TYR* 2.7 61.8 + - - -
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Residues in contact with TYR 215 (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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147B GLY* 3.2 21.7 - - - -
148B ASN 3.2 7.5 + - - -
149B ASN 2.9 26.9 - - - -
150B THR 3.4 19.1 - - - +
151B PRO* 3.4 35.0 - - + -
203B ARG* 3.1 27.2 + - - -
213B ASN* 3.5 29.8 + - + +
214B GLY* 1.3 78.9 - - - -
216B GLY* 1.3 64.2 - - - +
217B SER* 3.8 8.2 - - - +
234B PHE 3.0 8.7 - - - +
235B HIS* 3.1 33.2 - + + +
236B TYR* 3.3 6.0 + - - -
237B LYS* 5.4 4.7 - - + -
305B HIS* 6.2 2.2 - + - -
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Residues in contact with GLY 216 (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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145B LEU* 4.2 24.7 - - - -
146B VAL 4.1 2.8 - - - +
147B GLY* 4.6 2.7 - - - -
215B TYR* 1.3 71.8 - - - +
217B SER* 1.3 65.5 + - - +
218B HIS* 2.9 16.1 + - - -
220B PHE* 4.1 9.7 - - - -
234B PHE* 2.7 24.3 + - - +
236B TYR* 4.7 0.7 - - - -
600B HEM 3.6 12.5 - - - +
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Residues in contact with SER 217 (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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148B ASN* 4.4 6.9 + - - +
150B THR 3.0 23.7 + - - -
151B PRO* 3.7 22.0 - - - +
152B ILE 4.0 5.9 + - - -
215B TYR* 3.1 8.1 + - - +
216B GLY* 1.3 80.3 - - - +
218B HIS* 1.3 63.2 + - - -
233B LYS* 3.4 19.8 + - - +
234B PHE 5.3 0.8 - - - +
299B LEU* 3.4 21.9 - - - +
600B HEM 3.8 19.8 - - - +
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Residues in contact with HIS 218 (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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216B GLY 2.9 19.1 + - - -
217B SER* 1.3 77.9 + - - +
219B THR* 1.3 62.3 - - - +
220B PHE* 3.7 24.2 + + + -
232B CYS 3.9 1.7 - - - +
233B LYS* 3.7 16.8 - - - +
299B LEU* 3.6 20.4 - - + +
348B ASP* 2.6 27.2 + - - +
350B MET* 3.7 24.7 - - + -
351B LEU* 3.9 27.7 - - + +
354B ARG* 3.1 41.2 + - - -
600B HEM 3.8 10.3 - - + +
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Residues in contact with THR 219 (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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218B HIS* 1.3 74.3 - - - +
220B PHE* 1.3 69.9 + - - +
231B TYR* 3.8 27.1 - - + -
232B CYS 3.5 5.6 - - - +
233B LYS* 2.8 27.6 + - - +
296B PRO 2.9 17.7 + - - +
297B PHE* 3.9 19.7 - - + -
303B TRP* 3.7 10.3 - - + -
346B SER* 2.7 33.2 + - - -
348B ASP* 4.4 3.8 + - - -
351B LEU* 4.0 5.7 - - - +
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Residues in contact with PHE 220 (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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143B TRP* 6.2 1.8 - - - -
145B LEU* 4.3 14.8 - - + -
146B VAL 5.8 1.8 - - - -
216B GLY* 4.1 14.4 - - - -
218B HIS* 3.7 32.5 - + + -
219B THR* 1.3 76.4 - - - +
221B LYS* 1.3 62.9 + - - +
231B TYR* 3.3 10.2 - - - -
232B CYS* 2.9 36.5 + - - -
234B PHE* 3.7 40.8 - + + -
336B PRO* 5.3 6.3 - - + -
339B MET* 4.2 16.6 - - + -
343B ILE* 4.8 4.7 - - + -
344B GLU 3.7 15.9 - - - +
345B ALA 4.5 1.3 - - - -
346B SER* 4.5 1.3 - - - -
351B LEU* 4.0 28.9 - - + -
354B ARG* 5.4 2.2 - - - -
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Residues in contact with LYS 221 (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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220B PHE* 1.3 77.1 - - - +
222B LEU* 1.3 75.7 + - - +
223B VAL* 4.2 2.7 - - + -
229B ALA* 4.2 10.5 - - + -
230B VAL 3.5 9.2 - - - +
231B TYR* 4.3 16.4 - - + +
286B PHE* 4.8 1.3 - - + -
343B ILE* 3.6 5.0 - - - +
344B GLU* 2.9 64.9 + - + +
345B ALA 3.2 21.2 + - - +
421B HIS* 3.2 42.2 + - - +
423B ILE* 3.7 23.9 - - + +
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Residues in contact with LEU 222 (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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91B ILE* 5.8 2.5 - - + -
94B TYR* 3.7 25.8 - - + +
95B SER* 3.8 13.5 - - - -
100B PHE* 5.0 3.4 - - + -
220B PHE* 5.9 0.2 - - + -
221B LYS* 1.3 77.2 - - - +
223B VAL* 1.3 64.2 + - - +
228B GLU 3.6 0.3 - - - +
229B ALA* 3.0 6.9 - - - +
230B VAL* 2.7 44.8 + - + +
231B TYR 5.2 0.2 - - - +
232B CYS* 3.8 31.9 - - + -
234B PHE* 4.4 17.0 - - + -
281B ILE* 4.4 18.4 - - + -
283B VAL* 5.3 1.3 - - + -
342B GLY 3.3 13.2 - - - +
343B ILE* 3.9 17.9 - - + -
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Residues in contact with VAL 223 (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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94B TYR 3.4 4.9 - - - -
95B SER* 3.2 0.3 - - - -
96B LYS* 2.9 30.7 + - + +
221B LYS* 4.2 6.3 - - + -
222B LEU* 1.3 79.6 - - - +
224B ASN* 1.3 72.8 + - - +
227B GLY* 3.8 18.6 - - - +
228B GLU 3.2 8.5 - - - +
229B ALA* 4.0 9.0 - - + -
342B GLY* 2.9 24.1 + - - +
344B GLU* 3.9 13.9 - - + +
421B HIS* 3.8 29.2 - - + +
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Residues in contact with ASN 224 (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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92B THR 3.9 10.1 - - - +
93B LYS* 3.7 23.1 + - - +
94B TYR 3.3 12.9 + - - +
95B SER 4.1 0.2 - - - -
96B LYS* 3.9 10.6 + - - +
223B VAL* 1.3 78.6 - - - +
225B ALA* 1.3 52.5 + - - +
226B ASN* 2.5 31.4 + - - +
227B GLY* 2.7 13.0 + - - -
228B GLU* 2.7 69.3 + - - +
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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