Contacts of the helix formed by residues 325 - 335 (chain B) in PDB entry 1QQJ
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 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B ASN* 3.5 39.9 - - + +
277B PRO* 5.2 1.6 - - + -
293B TYR* 3.9 13.9 - - + +
294B THR* 3.9 9.9 - - - +
322B MET 5.6 0.7 - - - +
323B TYR 4.9 3.6 - - - +
324B TRP* 1.3 74.9 - - - +
326B MET* 1.3 59.8 + - - +
327B LEU* 3.3 10.6 + - - +
328B GLN* 3.0 36.7 + - - +
329B GLN* 2.9 31.8 + - - +
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Residues in contact with MET 326 (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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204B PHE* 3.4 43.2 - - + -
225B ILE* 3.8 15.4 - - + +
228B MET* 3.8 28.7 - - - +
266B MET* 3.9 4.5 - - + -
293B TYR* 3.9 14.7 + - + +
295B PHE* 3.5 38.4 - - + -
319B PHE* 3.8 22.4 - - + -
325B THR* 1.3 73.6 - - - +
327B LEU* 1.3 63.5 + - - +
329B GLN* 3.3 14.5 + - - +
330B LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 4.3 12.8 - - + +
221B ALA* 3.9 12.8 - - + +
222B HIS* 3.7 33.0 - - + +
225B ILE* 4.0 5.6 - - + -
289B HIS* 4.4 10.8 - - + -
291B GLN* 3.6 31.9 - - + +
293B TYR* 3.6 49.6 - - + -
325B THR* 3.2 6.5 - - - +
326B MET* 1.3 78.6 - - - +
328B GLN* 1.3 54.5 + - - +
331B THR* 2.7 38.1 + - - -
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Residues in contact with GLN 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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156B PRO* 4.3 2.2 - - - -
218B ILE* 4.0 10.1 - - + -
279B GLN* 2.9 40.5 + - - +
283B PRO* 4.1 1.4 - - - +
287B LEU* 2.9 41.3 + - + +
324B TRP* 3.3 26.6 - - + -
325B THR* 3.0 40.6 + - - +
327B LEU* 1.3 73.0 - - - +
329B GLN* 1.3 61.8 + - - +
331B THR* 4.4 0.4 - - - -
332B HIS* 2.8 32.6 + - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PHE* 3.5 52.1 - - + +
129B SER* 2.9 34.5 + - - +
156B PRO* 4.3 8.7 - - + -
204B PHE* 3.7 14.9 - - + -
322B MET* 6.1 0.2 - - - +
324B TRP* 3.9 5.9 + - + +
325B THR 2.9 19.6 + - - +
326B MET* 3.5 21.7 - - - +
328B GLN* 1.3 76.5 - - - +
330B LEU* 1.3 57.9 + - - +
332B HIS* 3.8 0.7 - - - +
333B HIS* 2.9 29.8 + - - +
346B LEU* 4.7 0.2 - - - -
347B ALA 4.8 2.5 - - - +
348B SER* 4.0 12.7 + - - +
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Residues in contact with LEU 330 (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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204B PHE* 3.9 24.5 - - + -
206B VAL* 4.3 10.1 - - + -
216B ILE* 3.7 24.7 - - + -
221B ALA* 3.7 37.2 - - + +
224B HIS* 4.0 19.5 - - + +
225B ILE* 4.3 6.7 - - + -
326B MET 3.0 17.2 + - - +
327B LEU 4.1 1.8 - - - +
329B GLN* 1.3 72.9 - - - +
331B THR* 1.3 65.0 + - - +
333B HIS* 3.3 4.1 + - - +
334B SER* 3.1 23.4 + - - -
340B LEU* 3.7 20.4 - - + +
346B LEU* 4.2 9.1 - - + +
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Residues in contact with THR 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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216B ILE 3.7 20.8 + - - +
217B PRO* 5.0 0.4 - - + -
218B ILE* 3.3 28.8 - - + +
221B ALA* 3.7 5.5 - - - +
286B TYR* 3.4 37.2 - - + +
287B LEU* 4.5 1.8 - - + -
327B LEU 2.7 22.7 + - - -
328B GLN* 3.7 5.4 - - - -
330B LEU* 1.3 74.2 - - - +
332B HIS* 1.3 66.0 + - - +
334B SER* 3.1 5.6 + - - -
335B VAL* 3.0 22.0 + - + +
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Residues in contact with HIS 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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179A GLN* 4.7 4.3 - - + -
243A GLU* 5.0 4.5 + - - +
250A PHE* 4.5 14.6 - + - -
251A LEU* 3.1 48.9 - - + +
127B PHE* 4.8 1.3 - + - -
155B LEU* 3.7 31.9 - - + +
156B PRO* 3.5 38.8 + - + +
157B VAL* 5.7 0.2 - - - -
286B TYR* 2.8 35.9 + - - -
287B LEU* 4.2 4.4 - - + +
328B GLN 2.8 21.8 + - - +
329B GLN 3.8 1.8 - - - +
331B THR* 1.3 73.0 - - - +
333B HIS* 1.3 63.9 + - - +
334B SER 3.1 1.2 + - - -
335B VAL* 3.2 8.1 + - + +
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Residues in contact with HIS 333 (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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162A ARG* 3.5 26.5 + - - -
250A PHE* 3.8 22.4 - + - -
251A LEU* 3.6 14.0 - - + +
254A SER* 5.3 0.4 - - - -
125B THR* 2.7 42.5 + - + +
127B PHE* 3.9 5.6 - + + -
160B HIS* 4.9 1.8 - + - -
329B GLN 2.9 18.1 + - - +
330B LEU* 3.6 9.2 - - - +
331B THR 3.2 0.4 - - - -
332B HIS* 1.3 77.1 - - - +
334B SER* 1.3 57.3 + - - +
338B CYS* 3.4 26.9 - - - +
340B LEU* 3.8 17.4 - - + +
346B LEU* 3.8 18.8 - - + +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASN* 3.8 14.4 - - - -
215B PRO* 3.3 12.8 - - - +
216B ILE* 3.2 33.0 + - - +
330B LEU 3.1 16.0 + - - -
331B THR 3.1 4.6 + - - -
333B HIS* 1.3 76.2 - - - +
335B VAL* 1.3 65.4 + - - +
336B ASN* 3.2 3.1 - - - -
337B GLY* 2.9 14.1 + - - -
338B CYS 3.6 19.3 - - - -
340B LEU* 4.4 4.0 - - - -
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A MET* 3.5 20.9 + - - +
178A GLY* 4.3 7.4 - - - -
190A TYR* 3.8 27.1 + - + +
251A LEU* 3.7 14.8 - - + -
215B PRO* 3.3 25.3 - - + +
286B TYR* 3.7 36.6 - - + +
331B THR* 3.0 14.2 + - + +
332B HIS* 3.2 16.5 + - + +
333B HIS 3.6 0.2 - - - -
334B SER* 1.3 78.3 - - - +
336B ASN* 1.3 58.6 + - - +
337B GLY 3.3 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