Contacts of the strand formed by residues 209 - 221 (chain A) in PDB entry 1QFG
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 GLU 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ALA 3.5 13.2 - - - +
202A ASN* 3.9 16.7 + - - +
203A ALA 3.8 1.1 - - - +
207A GLY 3.9 6.7 + - - +
208A SER* 1.3 78.0 - - - +
210A GLU* 1.3 67.5 + - - +
211A GLN* 4.1 13.4 + - + +
240A GLU* 3.5 35.2 - - + +
242A GLY* 3.3 23.0 + - - -
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LYS* 5.0 9.7 + - - +
83A ALA 5.0 5.9 - - - +
85A ASN* 4.8 17.3 + - - +
199A ARG* 3.4 31.0 + - - +
200A SER* 3.2 4.6 - - - -
201A ALA* 2.9 33.7 + - - +
202A ASN 5.1 1.6 - - - -
203A ALA* 3.9 25.2 - - + +
209A GLU* 1.3 78.4 - - - +
211A GLN* 1.3 68.1 + - - +
240A GLU* 3.2 6.1 - - - +
241A THR 3.5 24.1 - - - +
242A GLY* 4.1 3.0 - - - -
243A TYR 5.3 0.5 + - - -
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Residues in contact with GLN 211 (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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199A ARG* 3.5 7.9 - - - +
200A SER* 4.3 13.0 - - - +
209A GLU* 4.1 16.6 + - + -
210A GLU* 1.3 81.7 - - - +
212A ARG* 1.3 63.9 + - - +
213A TYR* 4.2 16.6 + - + +
238A GLU* 3.5 18.9 - - - +
239A PRO* 3.5 32.9 - - + +
240A GLU* 2.7 42.6 + - - +
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Residues in contact with ARG 212 (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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64A LYS 5.4 2.4 + - - -
65A SER* 6.1 1.8 - - - -
85A ASN* 4.7 18.5 + - - +
120A VAL* 3.6 22.0 - - - +
121A ILE 4.7 1.2 - - - -
122A ASP* 2.8 55.2 + - - +
123A PRO* 4.9 2.8 - - - +
197A LEU* 3.7 12.0 - - + +
198A ALA* 3.4 5.9 - - - -
199A ARG* 2.9 52.9 + - + +
211A GLN* 1.3 76.3 - - - +
213A TYR* 1.3 70.8 + - - +
214A ALA* 4.2 1.6 - - + -
236A GLN* 3.8 23.7 + - + +
237A ASN 3.6 3.1 - - - -
238A GLU* 2.9 32.9 + - + +
277A ARG* 4.2 1.2 - - - +
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Residues in contact with TYR 213 (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 LEU 3.5 2.2 - - - +
198A ALA* 3.7 27.6 - - + -
199A ARG 4.2 10.9 + - - -
200A SER* 5.2 2.8 - - - -
211A GLN* 4.2 17.5 + - + +
212A ARG* 1.3 82.4 - - - +
214A ALA* 1.3 62.3 + - - +
235A PHE 3.9 0.4 - - - +
236A GLN* 3.1 6.6 - - - +
237A ASN* 2.8 65.5 + - + +
239A PRO* 4.3 17.5 - - + -
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Residues in contact with ALA 214 (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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122A ASP* 5.3 0.2 - - + -
125A MET* 4.6 7.7 - - - +
195A THR 4.0 0.2 - - - +
196A GLY* 3.0 4.2 - - - -
197A LEU* 2.6 56.9 + - + +
212A ARG* 4.2 3.1 - - + -
213A TYR* 1.3 78.2 - - - +
215A ILE* 1.3 61.2 + - - +
234A TYR* 4.2 12.1 - - + +
235A PHE 3.4 7.9 - - - +
236A GLN* 3.9 20.0 - - + +
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Residues in contact with ILE 215 (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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125A MET* 4.6 1.6 - - - -
178A PHE* 3.6 28.0 - - + -
194A LEU* 4.0 24.0 - - + -
195A THR 3.1 16.8 - - - +
196A GLY* 3.7 3.8 - - - -
214A ALA* 1.3 71.4 - - - +
216A ALA* 1.3 59.6 + - - +
217A PRO* 3.4 6.6 - - + +
234A TYR* 4.8 0.9 - - - -
235A PHE* 2.9 50.4 + - + +
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Residues in contact with ALA 216 (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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125A MET* 3.5 28.6 - - + +
193A ARG 3.7 2.3 - - - +
194A LEU* 3.6 3.3 - - - -
195A THR* 2.7 33.7 + - - +
215A ILE* 1.3 70.5 - - - +
217A PRO* 1.3 65.8 - - - +
218A ALA* 3.7 1.8 + - + +
233A SER 3.3 15.7 - - - +
234A TYR* 3.8 9.0 - - + +
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Residues in contact with PRO 217 (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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193A ARG 3.6 0.7 - - - +
194A LEU* 3.5 27.4 - - + -
215A ILE* 3.4 13.9 - - + +
216A ALA* 1.3 90.9 - - - +
218A ALA* 1.3 58.0 + - - +
231A PHE* 4.0 5.4 - - + -
232A LEU 4.0 0.2 - - - -
233A SER* 2.5 50.9 + - - +
235A PHE* 4.0 16.2 - - + -
1014A MYR 4.4 27.8 - - + -
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Residues in contact with ALA 218 (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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154A LYS 4.4 7.9 - - - +
156A PRO* 3.9 21.5 - - + -
192A TYR* 3.3 5.4 - - - +
193A ARG* 2.8 40.3 + - + +
216A ALA* 3.7 2.2 + - + +
217A PRO* 1.3 72.8 - - - +
219A PHE* 1.3 62.2 + - - +
231A PHE* 3.1 13.2 - - - +
232A LEU* 4.3 14.6 - - + -
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Residues in contact with PHE 219 (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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156A PRO* 4.2 0.4 - - - -
184A LEU* 5.1 10.5 - - + -
190A TYR* 4.1 33.9 - + + -
191A SER 3.3 19.1 - - - -
192A TYR* 4.1 12.8 - - + -
218A ALA* 1.3 75.5 - - - +
220A THR* 1.3 70.7 + - - +
221A TRP* 4.7 7.9 - - + -
229A PHE* 3.7 5.4 - + - +
230A THR* 3.3 1.9 - - - -
231A PHE* 2.6 55.8 + - + +
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Residues in contact with THR 220 (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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155A ARG* 4.9 1.2 - - - +
156A PRO* 3.4 22.6 + - - +
188A GLY 5.9 0.7 - - - +
189A VAL 3.4 4.0 - - - +
190A TYR* 3.6 1.9 - - - -
191A SER* 2.7 48.5 + - - +
219A PHE* 1.3 77.7 - - - +
221A TRP* 1.3 73.5 + - - +
222A ARG* 3.8 28.9 + - + +
228A ASN* 4.0 9.9 + - - +
229A PHE 3.5 2.5 - - - -
230A THR* 2.9 22.5 + - - +
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Residues in contact with TRP 221 (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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189A VAL* 3.2 19.4 - - + +
190A TYR* 3.2 38.5 + + - -
219A PHE* 4.7 8.7 - + + -
220A THR* 1.3 78.3 - - - +
222A ARG* 1.3 56.1 + - - +
223A PRO* 3.5 32.3 - - + +
227A THR* 5.6 3.4 - - + -
228A ASN* 3.7 0.2 - - - -
229A PHE* 2.9 59.2 + + + +
286A PHE* 6.2 2.0 - + - -
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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