Contacts of the helix formed by residues 338 - 348 (chain A) in PDB entry 3QEL
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LEU* 4.0 18.2 - - + -
321A ASN 4.0 3.3 + - - +
322A ILE* 3.8 33.8 - - + -
323A THR* 2.9 32.0 + - - +
336A TRP* 3.2 23.3 - - + -
337A LYS* 1.3 76.5 - - - +
339A GLY* 1.3 58.5 + - - +
340A PRO 3.5 0.7 - - - -
341A LEU* 3.2 13.6 + - + +
342A PHE* 2.9 22.2 + - - +
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Residues in contact with GLY 339 (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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115A ARG* 3.3 25.8 - - - +
117A PRO* 4.4 1.6 - - - +
336A TRP* 2.8 29.3 + - - -
338A THR* 1.3 78.6 - - - +
340A PRO* 1.3 60.9 - - - +
342A PHE* 3.2 2.6 + - - +
343A LYS* 2.9 28.9 + - - +
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Residues in contact with PRO 340 (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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115A ARG* 4.3 13.7 - - + +
335A ILE* 4.6 13.5 - - + -
336A TRP 3.6 9.2 - - - +
337A LYS 3.7 11.2 - - - +
339A GLY* 1.3 89.3 - - - +
341A LEU* 1.3 56.3 + - - +
343A LYS* 3.5 3.0 + - + +
344A ARG* 3.1 19.9 + - - +
207B MET 4.7 6.5 - - - +
208B SER* 3.0 26.9 - - - +
209B LEU* 3.5 21.9 - - - +
210B ASP* 3.4 15.7 + - + +
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Residues in contact with LEU 341 (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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316A LEU* 3.8 15.7 - - + -
319A MET* 3.7 33.7 - - + -
320A GLU 5.5 1.6 - - - +
322A ILE* 4.0 14.1 - - + -
337A LYS 5.1 0.8 + - - +
338A THR* 3.2 16.0 + - + +
340A PRO* 1.3 74.7 - - - +
342A PHE* 1.3 67.9 + - - +
343A LYS 3.1 1.3 - - - -
344A ARG* 3.1 8.4 + - - +
345A VAL* 3.0 26.7 + - + +
210B ASP* 3.3 38.0 - - + +
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Residues in contact with PHE 342 (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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88A TYR* 3.1 34.3 - + + -
89A ALA* 3.9 12.3 - - + -
117A PRO* 3.6 13.0 - - + -
309A VAL* 4.6 2.9 - - + -
312A ALA* 3.9 26.5 - - + -
313A ILE* 3.2 34.3 - - + -
316A LEU* 4.0 25.0 - - + +
336A TRP* 3.8 18.4 - + + -
338A THR 2.9 13.3 + - - +
339A GLY 3.6 7.0 - - - +
341A LEU* 1.3 76.7 - - - +
343A LYS* 1.3 62.8 + - - +
345A VAL* 3.4 2.8 + - + +
346A LEU* 3.0 37.8 + - + +
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Residues in contact with LYS 343 (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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117A PRO* 4.3 12.2 - - + +
131A LYS* 4.6 12.1 - - - +
135A LEU 3.2 25.7 + - - -
136A SER* 3.8 24.8 - - - +
137A PHE 4.8 4.6 + - - +
138A LEU* 4.7 8.5 - - + -
339A GLY 2.9 16.0 + - - +
340A PRO* 3.7 6.5 - - + +
341A LEU 3.1 0.2 - - - -
342A PHE* 1.3 76.6 - - - +
344A ARG* 1.3 52.8 + - - +
346A LEU* 3.3 6.3 + - - +
347A MET* 2.8 67.3 + - + +
363A GLU 5.8 0.2 + - - -
364A ASP 6.1 1.6 - - - -
206B ASP* 5.3 0.6 + - - -
208B SER* 3.6 30.5 + - - +
209B LEU* 3.8 9.9 - - + +
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Residues in contact with ARG 344 (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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340A PRO 3.1 8.3 + - - +
341A LEU* 3.1 11.3 + - + +
343A LYS* 1.3 75.6 - - - +
345A VAL* 1.3 63.7 + - + +
347A MET* 3.5 5.5 + - + +
348A SER* 3.1 25.8 + - - +
209B LEU* 3.7 38.1 - - + +
210B ASP* 2.6 62.9 + - - +
213B ASP* 2.9 38.6 + - - +
215B LYS* 5.1 2.8 - - - +
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Residues in contact with VAL 345 (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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312A ALA* 3.7 31.4 - - + +
315A GLU* 3.8 28.7 - - + +
316A LEU* 4.3 13.9 - - + -
319A MET* 3.8 27.6 - - + -
341A LEU* 3.0 18.4 + - + +
342A PHE* 3.7 8.3 - - + +
344A ARG* 1.3 76.8 - - + +
346A LEU* 1.3 62.9 + - - +
348A SER* 3.3 8.8 + - - -
349A SER* 3.0 22.7 + - - +
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Residues in contact with LEU 346 (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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89A ALA* 5.3 1.6 - - + -
117A PRO* 3.7 33.0 - - + -
119A ILE* 4.2 10.1 - - + -
138A LEU* 4.1 20.0 - - + -
308A VAL* 4.5 10.5 - - + -
309A VAL* 4.3 20.2 - - + -
312A ALA* 3.4 22.7 - - + -
342A PHE* 3.0 38.6 + - + +
343A LYS* 3.5 6.7 - - - +
345A VAL* 1.3 72.0 - - - +
347A MET* 1.3 62.7 + - - +
348A SER 2.9 6.5 + - - -
349A SER* 3.0 20.9 + - - -
361A PHE* 3.5 11.9 - - + -
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Residues in contact with MET 347 (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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137A PHE 5.7 0.2 - - - +
138A LEU* 3.9 23.3 - - + -
343A LYS* 2.8 60.0 + - + +
344A ARG* 3.7 10.1 - - + +
345A VAL 3.4 0.4 - - - -
346A LEU* 1.3 72.9 - - - +
348A SER* 1.3 58.0 + - - +
349A SER 3.4 0.6 - - - +
361A PHE* 3.7 29.1 + - - +
362A ASN 3.7 13.6 - - - +
363A GLU* 3.3 30.1 - - - +
364A ASP 4.8 0.4 - - - -
365A GLY* 3.9 13.0 - - - +
209B LEU* 4.4 12.1 - - + -
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Residues in contact with SER 348 (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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315A GLU* 5.1 4.3 + - - -
344A ARG* 3.1 17.6 + - - +
345A VAL* 3.3 8.2 + - - -
346A LEU 3.0 0.2 - - - -
347A MET* 1.3 79.2 - - - +
349A SER* 1.3 67.1 + - - +
350A LYS* 3.8 4.3 + - - +
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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