Contacts of the strand formed by residues 267 - 274 (chain A) in PDB entry 1QMU
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 PHE 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A VAL 3.0 12.5 + - - +
176A LEU* 3.3 11.4 - - + +
177A SER 2.9 22.7 + - - -
206A ASP* 3.3 42.4 - - + -
209A VAL* 4.8 4.5 - - + -
210A PHE* 4.0 24.5 - + + -
213A LEU* 4.6 7.0 - - + -
261A TYR* 3.6 6.3 - + - -
265A ASN 3.2 21.3 - - - -
266A CYS* 1.3 76.6 - - - +
268A GLU* 1.3 59.8 + - - +
331A HIS* 3.3 27.6 - + - -
333A VAL* 5.0 5.8 - - + -
343A ARG* 3.6 16.4 - - - -
344A LEU* 4.2 32.3 - - + -
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Residues in contact with GLU 268 (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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68A LYS* 3.0 13.2 + - - -
70A ILE* 4.2 6.9 - - - +
177A SER* 2.4 33.0 + - - +
178A ALA 4.0 0.2 - - - +
179A ASN* 2.7 33.4 + - - +
190A PRO* 3.7 14.6 - - - +
210A PHE* 3.9 4.3 - - - -
256A MET* 3.5 5.0 - - - +
257A GLN* 3.3 30.8 + - - +
260A ASN* 3.2 35.3 + - + +
261A TYR* 5.1 1.6 - - - +
266A CYS 4.0 1.8 + - - -
267A PHE* 1.3 75.6 - - - +
269A VAL* 1.3 77.0 + - - +
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 6.3 0.7 - - + -
177A SER 3.3 8.7 + - - +
178A ALA* 3.1 7.3 - - + +
179A ASN 3.0 23.2 + - - -
187A VAL* 3.2 33.7 - - + -
188A ASN 3.5 2.9 - - - +
189A TYR* 3.9 24.2 - - + -
210A PHE* 4.1 13.2 - - + -
213A LEU* 4.9 8.1 - - + -
214A ALA* 4.8 10.5 - - + +
257A GLN* 3.9 0.9 - - - -
268A GLU* 1.3 81.9 - - - +
270A THR* 1.3 69.4 + - - +
271A ILE* 3.9 10.1 - - + -
298A PHE* 4.7 10.5 - - + -
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Residues in contact with THR 270 (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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144A ASN* 5.6 3.6 + - - +
179A ASN* 3.5 10.4 + - - +
181A HIS* 3.3 36.8 - - + +
187A VAL* 3.5 1.2 - - - -
188A ASN* 2.7 55.5 + - + +
192A ASP* 4.5 2.3 + - - -
249A TRP* 6.5 0.2 - - + -
257A GLN* 2.6 35.5 + - - +
269A VAL* 1.3 71.7 - - - +
271A ILE* 1.3 61.3 + - - +
272A GLU* 3.9 6.5 + - + +
998A SO4 5.1 5.2 - - - +
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Residues in contact with ILE 271 (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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69A TYR* 5.0 2.0 - - + -
178A ALA* 3.9 22.2 - - + -
179A ASN 3.0 8.7 + - - -
180A LEU* 3.5 17.8 - - + -
181A HIS* 2.7 31.8 + - - +
186A VAL 3.9 4.0 - - - +
187A VAL* 4.2 6.3 - - + +
217A TYR* 3.6 48.2 - - + -
224A MET* 4.5 3.1 - - + -
269A VAL* 3.9 15.9 - - + -
270A THR* 1.3 78.0 - - - +
272A GLU* 1.3 62.2 + - - +
273A LEU* 3.5 26.9 + - + +
298A PHE* 5.2 3.1 - - + -
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Residues in contact with GLU 272 (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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181A HIS* 3.3 21.7 - - + +
182A GLY 2.9 37.9 + - - +
183A GLY* 3.4 1.4 + - - -
184A SER* 3.0 37.0 - - - +
185A LEU* 3.1 5.9 - - - +
186A VAL* 2.8 38.4 + - + +
188A ASN* 5.5 0.7 - - + -
224A MET* 3.7 3.6 - - - +
249A TRP* 4.0 23.3 - - + -
250A TYR* 5.2 0.7 + - - -
270A THR* 5.1 7.7 - - + +
271A ILE* 1.3 71.9 - - - +
273A LEU* 1.3 58.3 + - - +
998A SO4 4.1 9.5 + - - -
999A ZN 3.9 7.4 - - - -
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Residues in contact with LEU 273 (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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79A VAL* 4.1 14.8 - - + -
80A GLY* 3.8 27.4 - - - +
83A LEU* 3.5 23.3 - - + -
180A LEU* 4.0 18.8 - - + -
181A HIS 3.0 14.0 + - - +
184A SER 3.5 0.2 + - - -
185A LEU* 3.2 16.3 - - - +
217A TYR* 3.3 15.0 - - + +
221A ASN* 5.2 0.2 + - - -
224A MET* 4.9 1.1 - - + -
271A ILE* 3.6 20.2 - - + +
272A GLU* 1.3 68.7 - - - +
274A GLY* 1.3 54.7 + - - +
287A TYR* 3.4 19.7 - - - -
290A GLN* 5.7 0.5 + - - -
291A ASN* 3.3 32.7 + - - +
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Residues in contact with GLY 274 (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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79A VAL* 5.8 0.8 - - - +
181A HIS 4.7 0.2 + - - -
182A GLY* 3.6 4.4 - - - -
183A GLY 2.7 28.1 + - - -
184A SER 2.5 20.5 + - - -
185A LEU* 3.4 10.7 - - - +
273A LEU* 1.3 76.3 - - - +
275A CYS* 1.3 57.9 + - - -
276A VAL 3.2 8.0 + - - +
287A TYR* 4.6 10.1 - - - -
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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