Contacts of the helix formed by residues 301 - 313 (chain A) in PDB entry 3QLD
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 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.7 4.0 - - + -
12A LEU* 4.0 22.7 - - + -
28A LYS* 5.5 1.8 - - + -
30A ALA* 3.6 31.4 - - + -
32A LEU* 3.9 8.3 - - + +
46A GLU* 2.6 20.6 + - - +
299A TYR 3.6 1.8 + - - -
300A GLU* 1.3 74.3 - - - +
302A GLY* 1.3 68.6 + - - +
303A VAL 3.1 8.1 + - - -
304A GLY 3.4 0.5 + - - -
305A ARG* 2.9 22.0 + - - +
330A PHE* 4.3 7.0 - - + -
333A ASP* 3.7 12.6 - - - -
334A VAL* 3.8 15.4 - - + +
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Residues in contact with GLY 302 (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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301A THR* 1.3 78.8 - - - +
303A VAL* 1.3 54.2 + - - +
305A ARG* 3.8 7.2 - - - +
306A VAL* 2.9 35.9 + - - +
333A ASP* 2.9 25.4 + - - -
334A VAL* 3.9 1.9 - - - +
335A LEU* 3.7 26.2 - - - -
339A ILE* 5.2 1.3 - - - -
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Residues in contact with VAL 303 (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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32A LEU* 4.0 16.4 - - + -
44A TRP* 4.1 10.8 - - + +
45A SER* 3.4 44.9 - - - +
46A GLU 3.8 0.2 - - - +
301A THR* 3.1 7.0 + - - +
302A GLY* 1.3 77.1 - - - +
304A GLY* 1.3 61.7 + - - +
306A VAL* 3.4 5.8 + - - +
307A HIS* 3.1 25.8 + - + -
334A VAL* 4.0 18.8 - - + +
335A LEU* 4.6 3.1 - - + -
355A VAL* 4.3 13.0 - - + +
359A VAL* 4.2 23.3 - - + -
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Residues in contact with GLY 304 (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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46A GLU* 3.1 32.0 + - - +
48A VAL* 5.4 3.1 - - - -
112A MSE 5.7 2.3 - - - +
300A GLU* 3.7 18.1 - - - +
303A VAL* 1.3 75.1 - - - +
305A ARG* 1.3 59.0 + - - +
307A HIS* 3.5 6.9 + - - +
308A GLY* 3.0 26.5 + - - -
323A LEU* 5.1 0.2 - - - +
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Residues in contact with ARG 305 (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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299A TYR* 4.0 1.4 - - - +
300A GLU* 2.9 45.0 + - + +
301A THR 2.9 20.4 + - - +
302A GLY* 3.8 6.1 - - - +
304A GLY* 1.3 72.9 - - - +
306A VAL* 1.3 59.2 + - - +
308A GLY 3.3 1.1 + - - +
309A LEU* 2.8 50.5 + - + +
323A LEU* 3.8 21.1 - - + +
324A GLY 2.9 33.3 + - - +
326A SER* 4.4 9.8 + - - +
329A TYR* 2.8 47.9 + - - -
330A PHE* 4.8 0.4 - - - -
333A ASP* 5.0 2.2 + - - -
339A ILE* 4.0 22.7 - - + -
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Residues in contact with VAL 306 (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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302A GLY 2.9 21.4 + - - +
303A VAL 3.7 4.3 - - - +
305A ARG* 1.3 75.0 - - - +
307A HIS* 1.3 60.4 + - + +
309A LEU* 3.3 5.8 + - - +
310A ILE* 3.0 36.8 + - + +
335A LEU* 4.0 4.9 - - + -
339A ILE* 3.6 28.3 - - + -
350A PRO* 3.9 24.2 - - + +
352A CYS* 4.0 13.9 - - - -
355A VAL* 4.2 16.6 - - + -
358A TRP* 4.0 15.3 - - + -
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Residues in contact with HIS 307 (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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44A TRP 3.1 25.3 + - - -
45A SER* 4.0 12.5 - - - -
46A GLU 5.0 1.2 + - - -
112A MSE 3.7 47.5 - - + +
116A ASP* 2.9 25.4 + - - +
126A LEU* 4.0 17.5 - - + +
270A PRO* 4.9 0.3 - - - +
276A PHE* 3.6 18.5 - + + -
303A VAL* 3.1 21.3 + - + +
304A GLY* 3.9 5.1 - - - +
306A VAL* 1.3 85.9 - - + +
308A GLY* 1.4 56.6 + - - +
310A ILE* 3.5 7.0 + - + +
311A ALA* 3.1 22.9 + - - +
355A VAL* 4.4 3.9 - - + +
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Residues in contact with GLY 308 (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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112A MSE 5.4 0.6 - - - +
270A PRO* 4.9 7.9 - - - -
295A VAL* 3.6 12.7 - - - +
304A GLY 3.0 14.4 + - - -
307A HIS* 1.4 73.2 - - - +
309A LEU* 1.3 61.5 + - - +
311A ALA* 3.5 5.4 + - - +
312A ALA* 3.0 26.2 + - - +
323A LEU* 3.4 21.3 - - - -
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Residues in contact with LEU 309 (chain A).
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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137A VAL* 4.1 24.6 - - + +
305A ARG* 2.8 32.7 + - + +
306A VAL* 3.7 7.2 - - - +
308A GLY* 1.3 77.2 - - - +
310A ILE* 1.3 61.2 + - - +
312A ALA* 3.2 13.1 + - - +
313A ALA* 3.3 11.4 + - - +
321A THR* 4.2 4.3 - - + -
323A LEU* 3.5 30.0 - - + +
339A ILE* 3.7 31.2 - - + -
347A ILE* 4.1 17.5 - - + -
349A VAL* 4.3 8.7 - - - +
350A PRO* 3.8 20.9 - - + -
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Residues in contact with ILE 310 (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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126A LEU* 4.2 28.3 - - + -
127A VAL* 3.8 31.7 - - + +
130A LEU* 3.9 22.7 - - + -
276A PHE* 4.6 2.5 - - + -
306A VAL* 3.0 27.2 + - + +
307A HIS* 3.6 10.3 - - + +
308A GLY 3.4 0.2 - - - -
309A LEU* 1.3 75.7 - - - +
311A ALA* 1.3 63.6 + - - +
313A ALA* 3.2 18.1 + - - +
314A LEU* 4.2 5.5 + - - +
349A VAL* 4.6 1.6 - - - -
350A PRO* 3.8 36.6 - - + +
352A CYS* 4.3 7.0 - - - +
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Residues in contact with ALA 311 (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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130A LEU* 6.0 0.9 - - - -
270A PRO* 3.6 31.2 - - + -
276A PHE* 4.6 8.7 - - + -
279A THR* 4.7 4.0 - - + -
295A VAL* 4.3 6.5 - - + -
307A HIS 3.1 11.1 + - - +
308A GLY 3.8 6.3 - - - +
309A LEU 3.4 0.2 - - - -
310A ILE* 1.3 77.2 - - - +
312A ALA* 1.3 57.6 + - - +
313A ALA 3.0 0.2 - - - -
314A LEU* 3.0 45.0 + - + +
317A MSE 3.4 10.9 - - + +
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Residues in contact with ALA 312 (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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134A ARG* 3.6 5.2 + - - -
137A VAL* 3.5 25.2 - - + +
295A VAL* 3.6 23.7 - - + +
308A GLY 3.0 14.6 + - - +
309A LEU* 3.2 14.3 + - - +
311A ALA* 1.3 75.1 - - - +
313A ALA* 1.3 57.8 + - - +
314A LEU 3.2 0.4 - - - -
317A MSE 3.4 20.5 - - + +
321A THR* 4.5 13.7 - - - -
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Residues in contact with ALA 313 (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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127A VAL* 3.6 23.6 - - + -
132A GLY* 3.9 2.7 - - - -
133A GLY 3.2 12.0 + - - -
134A ARG* 3.0 39.8 - - - +
137A VAL* 4.3 2.4 - - - +
309A LEU 3.3 3.4 + - - +
310A ILE 3.2 15.8 + - - +
311A ALA 3.0 0.4 - - - -
312A ALA* 1.3 74.3 - - - +
314A LEU* 1.3 61.6 + - - +
349A VAL* 3.7 19.3 - - + -
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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