Contacts of the strand formed by residues 214 - 224 (chain T) in PDB entry 1QTY
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 214 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210T THR* 3.0 5.0 - - - -
211T VAL 2.8 39.6 + - - +
212T ASN* 2.8 6.7 + - + +
213T GLY* 1.3 80.0 - - - +
215T LEU* 1.3 88.7 + - - +
216T TYR* 3.6 33.3 - + - +
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Residues in contact with LEU 215 (chain T).
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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208T GLU* 4.3 24.9 - - + +
209T ALA 3.6 3.6 - - - +
210T THR* 3.3 26.6 - - + +
213T GLY 4.0 1.6 + - - -
214T HIS* 1.3 92.6 + - - +
216T TYR* 1.3 65.7 + - - +
217T LYS* 3.5 33.5 - - - +
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Residues in contact with TYR 216 (chain T).
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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132T GLY* 4.4 12.3 + - - -
133T ARG* 4.2 17.4 + - + -
134T PRO* 3.4 33.2 - - + -
135T PHE* 3.9 18.2 - - + -
138T MET* 4.2 23.3 - - + -
208T GLU* 3.1 6.9 - - - +
209T ALA 2.8 37.6 + - - +
211T VAL* 3.9 19.2 + - + +
214T HIS* 3.6 46.5 - + + +
215T LEU* 1.3 73.0 - - - +
217T LYS* 1.3 67.8 + - - +
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Residues in contact with LYS 217 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T PHE* 4.0 2.4 - - - -
138T MET* 3.8 21.6 - - + +
139T TYR 4.0 5.0 - - - +
140T SER* 4.1 6.8 - - - -
206T THR* 3.6 11.0 - - + -
207T CYS 2.9 15.7 - - - +
208T GLU* 3.5 29.2 + - + +
215T LEU* 3.5 25.8 - - + +
216T TYR* 1.3 81.5 - - - +
218T THR* 1.3 61.7 + - - +
219T ASN* 4.5 8.0 + - - +
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Residues in contact with THR 218 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T PHE* 3.9 14.7 - - + -
137T GLU 3.3 9.0 - - - +
138T MET* 2.8 29.2 - - + -
139T TYR* 2.7 31.9 - - - +
158T CYS* 3.9 16.3 - - - +
205T LEU 4.0 0.2 - - - +
206T THR* 3.4 2.1 - - - -
207T CYS* 2.9 28.4 + - - +
217T LYS* 1.3 73.0 - - - +
219T ASN* 1.3 63.6 + - - +
220T TYR* 3.7 22.3 + - - +
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Residues in contact with ASN 219 (chain T).
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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18S MET* 4.4 21.2 - - + +
139T TYR* 2.8 31.1 + - - +
140T SER* 3.4 21.8 + - - +
141T GLU 5.3 0.8 + - - -
143T PRO* 3.2 12.7 - - + +
144T GLU 3.1 17.3 + - - -
204T LEU* 3.7 17.9 - - + -
205T LEU 3.4 3.8 - - - -
206T THR* 2.5 29.9 + - - +
217T LYS* 4.5 8.7 + - - +
218T THR* 1.3 75.5 - - - +
220T TYR* 1.3 68.3 + - - +
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Residues in contact with TYR 220 (chain T).
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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137T GLU* 3.6 21.1 + - - +
139T TYR* 3.1 30.1 - + - -
143T PRO* 3.7 3.8 - - - -
144T GLU* 3.3 19.3 - - + +
146T ILE* 3.3 28.5 - - + -
156T ILE* 3.4 23.8 - - + -
157T PRO* 3.8 20.2 + - + +
158T CYS* 3.8 33.1 - - + -
204T LEU* 3.0 6.4 - - - +
205T LEU* 2.7 38.2 + - + +
207T CYS* 4.5 1.1 - - - -
218T THR* 3.7 23.7 + - - -
219T ASN* 1.3 77.3 - - - +
221T LEU* 1.3 61.6 + - - +
222T THR* 4.1 1.1 - - - +
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Residues in contact with LEU 221 (chain T).
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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48R LYS* 3.5 37.7 - - + -
81R MET* 4.3 2.2 - - - -
17S PHE* 3.7 29.6 - - + -
21S TYR* 4.3 19.1 - - + +
62S ASN* 5.9 1.6 - - + -
143T PRO* 3.8 17.7 - - + +
144T GLU 3.0 7.4 + - - +
145T ILE* 3.4 21.4 - - + +
146T ILE* 3.0 20.8 + - - -
203T GLY* 3.4 17.7 - - - +
204T LEU* 4.7 4.3 - - + -
220T TYR* 1.3 73.1 - - - +
222T THR* 1.3 72.8 + - - +
223T HIS 3.4 1.0 + - - -
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Residues in contact with THR 222 (chain T).
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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48R LYS* 4.2 3.5 - - - -
146T ILE* 3.3 21.3 - - + +
148T MET* 4.1 12.3 - - - -
154T LEU* 3.9 22.0 - - + -
156T ILE* 4.9 1.3 - - + -
201T GLU 3.0 3.5 + - - +
202T ILE* 3.0 21.1 - - - +
203T GLY* 2.5 44.8 + - - -
205T LEU* 3.4 26.9 - - + -
221T LEU* 1.3 81.3 - - - +
223T HIS* 1.3 59.5 + - - +
224T ARG 4.1 0.7 - - - -
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Residues in contact with HIS 223 (chain T).
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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46R ILE* 4.0 32.9 - - + +
48R LYS* 3.8 25.4 + - - +
83R ILE* 3.8 23.9 - - + +
85R PRO* 6.4 0.2 - - - +
62S ASN 5.1 1.1 + - - -
63S ASP* 4.8 3.7 + - - -
145T ILE* 4.0 18.2 - - + -
146T ILE 3.1 8.3 + - - +
147T HIS* 3.4 17.7 - + + +
148T MET* 3.2 19.5 + - - -
221T LEU 3.4 0.8 + - - -
222T THR* 1.3 72.4 - - - +
224T ARG* 1.3 78.7 + - - +
225T GLN* 3.4 28.8 + - - -
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Residues in contact with ARG 224 (chain T).
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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63S ASP* 2.8 43.8 + - - +
65S GLY* 3.3 28.4 + - - +
66S LEU* 4.1 11.1 - - - +
106S PRO* 5.4 0.6 - - - +
148T MET* 3.5 28.1 - - + +
149T THR* 5.8 0.4 - - - +
150T GLU* 3.4 32.7 - - - +
199T TYR* 6.1 0.6 - - - +
202T ILE* 4.2 15.0 - - + +
222T THR 4.1 1.8 + - - -
223T HIS* 1.3 83.1 + - - +
225T GLN* 1.3 70.5 + - - +
182X LYS* 3.3 29.9 - - - +
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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