Contacts of the strand formed by residues 219 - 228 (chain B) in PDB entry 3QGT
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 THR 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ASN* 3.8 16.8 - - - +
187B ILE* 4.0 8.1 - - + -
188B ASN 3.2 11.0 + - - -
189B SER* 2.8 31.7 + - - +
191B TYR* 4.2 7.0 - - - +
215B THR* 3.4 4.6 - - - +
216B SER 2.9 36.8 + - - +
217B ASN* 4.2 4.3 - - + +
218B ASN* 1.3 80.5 - - - +
220B THR* 1.3 76.6 + - - +
221B LEU* 3.7 0.9 - - - +
573B THR* 5.4 4.7 - - - -
595B ASN* 6.1 0.9 - - - +
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Residues in contact with THR 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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188B ASN* 3.1 28.8 + - - +
213B VAL* 4.1 6.3 - - - -
214B TYR 2.9 8.1 - - - -
215B THR* 3.4 4.0 - - - +
219B THR* 1.3 88.7 + - - +
221B LEU* 1.3 66.3 + - - +
364B GLN 3.3 24.7 - - - +
365B TYR* 4.2 7.0 - - + -
570B PRO* 4.7 0.7 - - - +
571B PHE 2.8 26.4 + - - +
572B PRO* 4.7 0.3 - - - +
573B THR* 3.3 31.4 - - + +
595B ASN* 5.6 0.3 - - - +
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Residues in contact with LEU 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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51B ASN* 3.9 25.8 - - - +
53B LEU* 4.0 18.2 - - + -
54B ASP* 4.4 2.9 - - + +
185B THR* 4.3 1.1 - - + -
186B ARG 3.1 18.8 - - - +
187B ILE* 4.2 15.9 - - + -
188B ASN 4.5 0.2 - - - +
213B VAL* 3.6 3.5 - - - +
214B TYR* 2.8 49.6 + - - +
216B SER* 4.0 11.0 - - - +
219B THR 3.7 10.1 - - - +
220B THR* 1.3 80.8 - - - +
222B ASP* 1.3 63.5 + - - +
223B PHE* 3.9 30.1 - - + -
570B PRO* 4.6 3.8 - - - +
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Residues in contact with ASP 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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185B THR* 3.7 2.9 - - - +
186B ARG* 2.7 70.6 + - - +
210B VAL* 6.3 0.4 - - - -
211B SER* 3.8 9.6 - - - +
212B ASP 3.8 14.6 - - - +
213B VAL* 4.3 8.3 - - + -
221B LEU* 1.3 75.5 - - - +
223B PHE* 1.3 70.7 + - - +
224B ILE* 4.1 3.6 + - - +
323B HIS* 4.0 5.9 - - - -
569B TYR 4.0 0.7 - - - -
570B PRO* 3.1 26.3 - - - +
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Residues in contact with PHE 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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293A PHE* 3.6 8.8 - + + -
295A PHE* 3.4 32.5 - + - -
53B LEU* 4.4 7.2 - - + -
54B ASP* 3.8 5.6 - - - -
57B TYR* 3.3 52.9 - + + +
184B PHE 3.8 3.6 - - - +
185B THR* 3.0 42.8 - - + -
211B SER* 2.8 47.5 + - - +
214B TYR* 4.0 18.6 - + - -
221B LEU* 3.9 18.6 - - + -
222B ASP* 1.3 75.0 - - - +
224B ILE* 1.3 62.3 + - - +
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Residues in contact with ILE 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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34B ASN* 5.2 0.7 - - - +
57B TYR* 5.6 0.6 + - - -
182B ILE 3.6 0.9 - - - +
183B TYR* 3.8 1.9 - - - -
184B PHE* 2.9 49.8 + - + +
186B ARG* 3.4 53.8 - - + +
207B ILE* 4.0 17.0 - - + -
209B SER 3.3 7.4 - - - +
210B VAL* 3.7 19.5 - - + -
222B ASP* 4.1 1.3 - - - +
223B PHE* 1.3 78.1 - - - +
225B ILE* 1.3 62.9 + - - +
226B TYR* 3.4 34.3 - - + +
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Residues in contact with ILE 225 (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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289A ASP* 3.5 38.1 - - + +
292A TYR* 5.4 0.4 - - + -
293A PHE* 3.9 28.0 - - + -
57B TYR* 4.8 1.1 - - - +
181B LYS* 4.0 18.6 - - + -
182B ILE 4.0 2.0 - - - -
183B TYR* 4.0 24.7 - - + -
207B ILE* 3.4 3.9 - - - -
208B ILE* 2.8 53.8 + - + +
209B SER* 3.1 15.2 + - - +
224B ILE* 1.3 76.7 - - - +
226B TYR* 1.3 67.3 + - - +
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Residues in contact with TYR 226 (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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34B ASN* 3.5 38.0 + - + +
181B LYS* 3.2 10.0 - - - +
182B ILE* 2.9 49.0 + - + +
184B PHE* 3.6 39.9 - + + -
200B ILE* 3.8 35.9 - - + +
205B TYR* 4.6 9.4 - - + -
206B GLN* 3.5 6.3 - - - -
207B ILE* 3.5 26.9 - - + -
224B ILE* 3.4 28.9 - - + +
225B ILE* 1.3 73.5 - - - +
227B LYS* 1.3 59.2 + - - +
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Residues in contact with LYS 227 (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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286A GLU* 4.1 20.1 + - - +
180B LYS* 4.0 10.0 - - + +
181B LYS* 3.4 29.6 - - + +
205B TYR* 3.1 11.0 - - - -
206B GLN* 2.6 37.4 + - + +
208B ILE* 3.5 42.2 - - + -
225B ILE 3.8 0.2 + - - -
226B TYR* 1.3 74.8 - - - +
228B LYS* 1.3 68.9 + - + +
229B THR* 3.1 4.5 + - - -
230B ASN* 4.3 23.5 + - - +
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Residues in contact with LYS 228 (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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6B CYS* 4.8 7.9 - - - -
7B ASP* 4.7 13.7 - - - +
177B LYS* 3.8 35.7 - - - +
179B ILE 3.9 7.6 - - - +
180B LYS* 3.0 27.8 + - + +
204B GLU* 3.5 27.9 + - - +
205B TYR* 3.4 29.2 + - + +
227B LYS* 1.3 78.1 - - - +
229B THR* 1.3 62.8 + - - +
230B ASN* 2.7 33.2 + - - +
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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