Contacts of the helix formed by residues 320 - 333 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.9 18.1 - - - +
16B ALA* 4.4 10.5 - - - +
35B GLU* 2.4 34.5 + - - -
319B SER* 1.3 73.9 - - - +
321B PRO* 1.3 77.9 - - - +
322B VAL* 3.1 8.9 + - - +
323B GLY 3.5 0.3 + - - -
324B THR* 2.5 30.3 + - - -
350B TRP* 3.2 11.9 - - - +
353B PHE* 4.6 10.1 - - - +
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Residues in contact with PRO 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B SER* 1.3 92.5 - - - +
322B VAL* 1.3 56.1 + - - +
324B THR* 4.2 0.4 - - - -
325B VAL* 2.7 37.3 + - + +
350B TRP* 3.0 57.0 - - + +
351B GLU* 4.3 6.5 - - - +
353B PHE* 3.9 14.6 - - + -
354B VAL* 3.6 23.3 - - + -
361B VAL* 4.6 12.1 - - + -
377B LEU* 3.6 1.7 - - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.6 11.2 - - + -
33B LEU* 3.6 34.5 - - + +
34B GLY* 3.8 13.0 - - - +
35B GLU* 3.6 34.3 - - + +
94B THR* 5.5 1.3 - - + -
320B SER* 3.1 5.9 + - - +
321B PRO* 1.3 78.4 - - - +
323B GLY* 1.3 70.8 + - - +
325B VAL* 4.0 1.7 - - - +
326B ALA* 3.3 17.2 + - - +
353B PHE* 6.1 0.7 - - + -
354B VAL* 3.8 18.6 - - + -
375B LEU* 5.0 6.7 - - + +
377B LEU* 4.0 8.8 - - + +
379B LEU* 5.2 3.4 - - + -
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Residues in contact with GLY 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 2.9 33.0 + - - -
94B THR* 5.9 2.0 - - - -
290B VAL* 5.9 1.0 - - - +
291B ALA* 5.3 5.4 - - - -
317B ASN* 4.6 1.6 - - - -
319B SER* 4.0 12.1 - - - -
322B VAL* 1.3 73.2 - - - +
324B THR* 1.3 64.0 + - - +
326B ALA* 3.2 9.3 + - - +
327B ALA* 3.0 21.9 + - - +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 5.1 2.9 - - + -
317B ASN* 3.3 26.2 + - - +
319B SER* 2.9 17.7 + - - -
320B SER 2.5 22.9 + - - -
321B PRO 3.9 1.8 - - - -
323B GLY* 1.3 74.4 - - - +
325B VAL* 1.3 63.4 + - + +
327B ALA* 3.1 17.3 - - - +
328B ALA* 3.2 5.5 + - - +
340B LEU* 3.9 7.6 - - + +
341B GLU 5.1 3.6 - - - +
342B TRP* 5.4 5.0 - - + -
350B TRP* 3.4 20.3 - - + -
362B ILE* 5.8 0.2 - - + -
367B ILE* 3.9 23.8 - - + -
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO* 2.7 28.8 + - + +
323B GLY 3.3 0.2 - - - -
324B THR* 1.3 73.7 - - + +
326B ALA* 1.3 67.5 + - - +
328B ALA* 2.8 19.1 + - + +
329B HIS* 3.1 17.6 + - + -
356B TYR* 4.3 15.0 - - + +
361B VAL* 4.0 27.6 - - + -
367B ILE* 5.2 4.5 - - + -
369B LEU* 4.2 24.0 - - + -
375B LEU* 4.4 7.9 - - + +
377B LEU* 3.6 21.5 - - + -
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 3.8 28.7 - - + -
290B VAL* 5.4 2.5 - - + -
296B LEU* 4.2 18.5 - - + +
322B VAL 3.3 8.4 + - - +
323B GLY* 3.2 10.5 + - - +
325B VAL* 1.3 77.0 - - - +
327B ALA* 1.3 64.0 + - - +
329B HIS* 2.9 30.8 + - - +
330B VAL* 3.3 9.5 + - - +
375B LEU* 4.8 9.5 - - + +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 4.4 26.6 - - + +
315B PRO* 5.2 2.1 - - + +
317B ASN* 3.9 11.0 - - - +
323B GLY 3.0 11.3 + - - +
324B THR 3.1 14.1 - - - +
326B ALA* 1.3 76.4 - - - +
328B ALA* 1.3 54.7 + - - +
330B VAL* 3.3 6.3 + - - +
331B CYS* 2.9 31.8 + - - -
340B LEU* 3.8 20.0 - - + -
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL* 3.8 28.9 - - + +
324B THR 3.2 6.6 + - - +
325B VAL* 2.8 11.7 + - - +
327B ALA* 1.3 76.9 - - - +
329B HIS* 1.3 66.2 + - - +
331B CYS* 3.4 12.3 - - - +
332B ALA* 2.9 23.7 + - - +
340B LEU* 4.0 3.3 - - + +
367B ILE* 4.5 15.9 - - + -
369B LEU* 4.0 11.5 - - + +
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Residues in contact with HIS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B PRO* 4.4 2.7 - - + -
108B VAL* 3.2 34.1 - - + -
109B TYR* 3.1 56.8 + + - +
112B LEU* 4.6 3.1 - - + -
325B VAL* 3.1 21.9 + - + -
326B ALA* 2.9 16.9 + - - +
328B ALA* 1.3 77.6 - - - +
330B VAL* 1.3 62.1 + - - +
332B ALA* 3.2 13.2 + - - +
333B ALA* 3.2 11.6 + - - +
369B LEU* 3.5 17.5 - - + +
370B THR 5.2 0.2 - - - -
375B LEU* 2.9 44.0 + - + -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.9 13.0 - - + -
290B VAL* 4.8 9.2 - - + -
296B LEU* 3.5 45.8 - - + +
299B ALA* 4.4 3.4 - - + -
300B LYS* 4.2 26.9 - - + +
313B PHE* 4.0 24.5 - - + -
326B ALA 4.0 3.6 - - - +
327B ALA* 3.3 8.9 + - - +
328B ALA 3.2 0.2 - - - -
329B HIS* 1.3 72.9 - - - +
331B CYS* 1.3 64.9 + - - +
332B ALA 3.0 2.8 + - - -
333B ALA* 3.1 12.1 + - - +
334B VAL* 3.3 16.2 + - + +
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Residues in contact with CYS 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ARG* 2.9 22.0 + - - -
120B VAL* 4.0 10.8 - - + -
313B PHE* 5.0 2.5 - - - -
315B PRO* 4.1 15.3 - - - -
327B ALA 2.9 29.9 + - - -
328B ALA* 3.4 13.7 - - - +
330B VAL* 1.3 77.3 - - - +
332B ALA* 1.3 57.1 + - - +
334B VAL* 3.7 5.8 - - - +
337B PHE* 3.3 51.7 - - + +
340B LEU* 4.0 13.0 - - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B TYR* 4.4 9.0 - - + -
115B ALA* 4.2 10.5 - - + -
116B PHE* 2.8 32.4 + - - +
117B ARG* 3.4 28.3 + - + +
118B ARG* 5.5 0.9 - - - -
120B VAL* 4.6 4.7 - - + +
328B ALA 2.9 11.6 + - - +
329B HIS* 3.3 11.7 - - - +
330B VAL 3.0 0.2 - - - -
331B CYS* 1.3 78.9 - - - +
333B ALA* 1.3 56.1 + - - +
334B VAL 3.2 6.0 + - - -
369B LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 4.5 2.7 - - + +
112B LEU* 3.5 31.7 - - + +
113B GLY 6.0 0.3 - - - -
114B GLY 3.2 21.3 - - - +
116B PHE* 3.4 15.1 - - - -
300B LYS* 4.0 14.7 - - + -
329B HIS 3.2 9.6 + - - +
330B VAL* 3.1 8.5 + - - +
332B ALA* 1.3 77.1 - - - +
334B VAL* 1.3 63.8 + - + +
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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