Contacts of the helix formed by residues 320 - 333 (chain A) in PDB entry 2QQ6
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 SER 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ILE* 4.0 20.0 - - - +
16A ALA* 4.7 5.9 - - - +
35A GLU* 2.6 30.9 + - - -
319A SER* 1.3 70.7 - - - +
321A PRO* 1.3 78.4 - - - +
322A VAL* 2.9 18.5 + - - +
323A GLY 3.6 0.2 + - - -
324A THR* 2.8 24.4 + - - -
350A TRP* 3.3 10.1 - - - +
353A PHE* 4.3 10.1 - - - +
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Residues in contact with PRO 321 (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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320A SER* 1.3 93.2 - - - +
322A VAL* 1.3 51.5 + - - +
324A THR* 3.7 0.4 - - - -
325A VAL* 2.7 41.0 + - + +
350A TRP* 3.2 60.3 - - + +
351A GLU* 4.2 6.3 - - - +
353A PHE* 3.8 11.0 - - + -
354A VAL* 4.1 19.1 - - + -
361A VAL* 4.0 19.1 - - + -
377A LEU* 4.5 1.1 - - - -
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Residues in contact with VAL 322 (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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22A LEU* 4.5 8.1 - - + -
33A LEU* 4.2 41.5 - - + +
34A GLY* 4.5 0.4 - - - -
35A GLU* 3.1 21.3 - - + +
94A THR* 5.7 1.8 - - + -
320A SER* 2.9 12.0 + - - +
321A PRO* 1.3 73.4 - - + +
323A GLY* 1.3 71.0 + - - +
324A THR 3.0 0.9 - - - -
325A VAL* 2.7 15.9 + - - +
326A ALA* 2.9 10.4 + - - +
353A PHE* 5.4 2.0 - - + +
354A VAL* 3.9 24.2 - - + -
375A LEU* 5.0 4.6 - - + +
377A LEU* 3.6 17.9 - - + +
379A LEU* 5.7 1.6 - - + -
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Residues in contact with GLY 323 (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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35A GLU* 2.8 27.7 + - - -
94A THR* 6.0 0.4 - - - -
290A VAL* 5.5 1.7 - - - +
291A ALA* 5.1 8.3 - - - +
317A ASN* 4.3 1.6 - - - -
319A SER* 3.5 18.6 - - - -
320A SER 3.6 0.2 + - - -
322A VAL* 1.3 73.4 - - - +
324A THR* 1.3 61.4 + - - +
326A ALA* 3.1 24.2 + - - +
327A ALA* 3.1 9.4 + - - +
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Residues in contact with THR 324 (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 LEU* 5.7 1.1 - - + -
317A ASN* 2.8 32.4 + - - +
319A SER* 3.4 8.9 + - - -
320A SER 2.8 21.7 + - - -
321A PRO 3.7 5.6 - - - +
322A VAL 3.0 0.8 - - - -
323A GLY* 1.3 75.9 - - - +
325A VAL* 1.3 57.0 + - + +
327A ALA* 3.5 1.9 + - - +
328A ALA* 3.0 22.2 + - - +
340A LEU* 3.7 11.5 - - + +
341A GLU 5.3 0.7 - - - +
342A TRP* 5.2 5.0 - - + -
350A TRP* 3.5 17.5 - - + -
367A ILE* 3.4 28.9 - - + -
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Residues in contact with VAL 325 (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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321A PRO 2.7 25.3 + - - +
322A VAL 2.7 8.0 + - - +
324A THR* 1.3 72.1 - - + +
326A ALA* 1.3 69.8 + - - +
328A ALA* 3.4 5.7 - - + +
329A HIS* 3.0 30.8 + - + -
356A TYR* 4.6 6.1 - - + -
361A VAL* 3.9 25.4 - - + -
367A ILE* 5.4 2.0 - - + -
369A LEU* 3.9 21.3 - - + -
375A LEU* 3.7 24.0 - - + +
377A LEU* 3.9 24.2 - - + -
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Residues in contact with ALA 326 (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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94A THR* 3.8 29.6 - - + +
290A VAL* 5.0 3.1 - - + -
296A LEU* 3.8 16.0 - - + +
322A VAL 2.9 9.2 + - - +
323A GLY* 3.1 15.5 - - - +
325A VAL* 1.3 81.2 - - - +
327A ALA* 1.3 61.2 + - - +
329A HIS* 3.0 17.8 + - - +
330A VAL* 3.3 8.3 + - - +
375A LEU* 4.0 16.2 - - + +
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Residues in contact with ALA 327 (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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290A VAL* 3.6 31.1 - - + +
315A PRO* 5.1 0.2 - - + -
317A ASN* 5.3 4.9 - - + -
323A GLY 3.1 8.0 + - - +
324A THR* 3.7 9.6 - - - +
326A ALA* 1.3 76.8 - - - +
328A ALA* 1.3 65.3 + - - +
330A VAL* 2.8 6.1 + - - +
331A CYS* 2.8 28.7 + - - -
340A LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 328 (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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120A VAL* 3.8 23.6 - - + +
324A THR 3.0 15.5 + - - +
325A VAL* 3.1 13.2 + - - +
327A ALA* 1.3 74.6 - - - +
329A HIS* 1.3 64.0 + - - +
331A CYS* 3.4 6.6 + - - +
332A ALA* 3.0 18.0 + - - +
340A LEU* 3.9 10.5 - - + +
367A ILE* 4.2 9.2 - - + -
369A LEU* 3.4 25.2 - - + +
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Residues in contact with HIS 329 (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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107A PRO* 4.6 2.9 - - + -
108A VAL* 3.8 22.4 - - + -
109A TYR* 3.3 48.3 + + - +
112A LEU* 4.2 4.4 - - + +
296A LEU* 4.7 0.4 - - + -
325A VAL* 3.0 28.9 + - + -
326A ALA 3.1 10.8 - - - +
328A ALA* 1.3 77.1 - - - +
330A VAL* 1.3 61.3 + - - +
332A ALA* 3.1 12.8 + - - +
333A ALA* 3.4 9.4 + - - +
369A LEU* 3.7 20.4 - - + +
370A THR 5.8 0.4 - - - -
375A LEU* 3.1 54.7 + - + -
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Residues in contact with VAL 330 (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 LEU* 4.1 9.4 - - + -
290A VAL* 4.3 8.1 - - + -
296A LEU* 3.5 44.0 - - + +
299A ALA* 4.0 20.6 - - + -
300A LYS* 4.0 19.9 - - + +
313A PHE* 4.1 15.9 - - + -
326A ALA 3.6 5.6 - - - +
327A ALA* 2.8 17.8 + - - +
329A HIS* 1.3 72.4 - - - +
331A CYS* 1.3 64.0 + - - +
333A ALA* 2.9 15.6 + - - +
334A VAL* 3.3 11.8 + - + +
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Residues in contact with CYS 331 (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 ARG* 3.5 8.7 + - - -
120A VAL* 4.0 10.3 - - + -
313A PHE* 4.7 4.7 - - - -
315A PRO* 3.4 23.6 - - - -
327A ALA* 2.8 28.2 + - - +
328A ALA 3.7 5.2 - - - +
330A VAL* 1.3 73.0 - - - +
332A ALA* 1.3 59.8 + - - +
334A VAL* 3.6 8.0 - - - +
337A PHE* 3.3 62.6 - - + +
340A LEU* 4.1 9.9 - - - -
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Residues in contact with ALA 332 (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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109A TYR* 4.7 4.0 - - + -
115A ALA* 4.3 7.2 - - + -
116A PHE* 2.6 36.8 + - - +
117A ARG* 3.4 31.7 + - + +
120A VAL* 4.5 2.9 - - + -
328A ALA 3.0 13.0 + - - +
329A HIS 3.4 9.2 - - - +
330A VAL 3.0 1.6 + - - -
331A CYS* 1.3 79.5 - - - +
333A ALA* 1.3 50.7 + - - +
334A VAL 3.3 1.8 - - - -
369A LEU* 3.8 16.2 - - + -
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Residues in contact with ALA 333 (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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109A TYR* 4.4 1.1 - - + +
112A LEU* 3.8 34.0 - - + +
113A GLY 5.1 1.1 - - - -
114A GLY 3.3 23.1 - - - +
116A PHE* 3.6 20.6 - - - -
300A LYS* 4.3 14.7 - - + -
304A ASN* 5.6 0.2 - - - +
329A HIS 3.4 5.7 + - - +
330A VAL 2.9 8.8 + - - +
332A ALA* 1.3 76.2 - - - +
334A VAL* 1.3 61.3 + - + +
335A SER 4.1 0.2 + - - -
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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