Contacts of the helix formed by residues 338 - 352 (chain B) in PDB entry 1Q6X
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 ASP 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TRP* 4.2 6.9 - - - -
164B GLN* 2.8 21.5 + - - +
334B HIS* 3.4 20.2 - - + -
337B PHE* 1.3 76.8 - - - +
339B GLY* 1.3 67.3 + - - +
340B ILE* 3.3 8.9 + - + +
341B VAL* 3.4 5.3 + - - +
342B LEU* 3.3 17.9 + - - +
448B SER* 5.8 1.1 - - - +
458B ARG* 3.0 38.8 + - - +
459B VAL* 3.6 28.7 - - + +
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 6.6 0.4 - - - -
334B HIS* 4.6 6.9 + - - -
338B ASP* 1.3 72.7 - - - +
340B ILE* 1.3 59.9 + - - +
342B LEU* 3.6 11.9 - - - +
343B VAL* 2.9 37.8 + - - +
552B VAL* 4.9 16.2 - - - -
560B CYS* 5.8 4.9 - - - -
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Residues in contact with ILE 340 (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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338B ASP* 3.3 6.6 + - + -
339B GLY* 1.3 76.7 - - - +
341B VAL* 1.3 64.2 + - + +
343B VAL* 3.4 3.3 + - - +
344B GLN* 3.1 42.8 + - + +
450B SER* 5.6 10.1 - - - -
452B ARG* 4.4 22.7 - - - +
551B GLN 4.3 17.7 - - - +
552B VAL* 5.1 3.4 - - + -
553B PRO* 4.4 17.3 - - + -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLN* 3.7 33.0 - - + +
165B TYR* 3.7 62.8 - - + +
168B LEU* 4.4 11.7 - - + -
337B PHE* 4.7 2.7 - - + -
338B ASP* 3.4 8.1 + - - +
340B ILE* 1.3 75.7 - - + +
342B LEU* 1.3 67.0 + - - +
344B GLN* 3.2 2.4 + - - +
345B CYS* 3.1 21.5 + - - +
452B ARG* 4.2 18.8 - - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PRO* 5.5 6.5 - - + +
110B VAL* 3.6 28.3 - - + -
168B LEU* 4.8 6.7 - - + -
318B LEU* 3.5 31.9 - - + -
330B VAL* 5.0 6.3 - - + +
332B CYS* 3.8 22.4 - - + -
337B PHE* 4.2 13.4 - - + -
338B ASP 3.3 11.0 + - - +
339B GLY* 3.3 15.0 + - - +
341B VAL* 1.3 80.8 - - - +
343B VAL* 1.3 58.0 + - + +
345B CYS* 3.2 8.5 + - + +
346B THR* 2.9 47.4 + - + +
560B CYS* 5.7 3.4 - - - -
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.9 13.7 - - + -
339B GLY* 2.9 20.2 + - - +
340B ILE* 3.8 4.9 - - - +
342B LEU* 1.3 78.1 - - + +
344B GLN* 1.3 67.0 + - - +
346B THR* 3.0 6.2 + - - -
347B GLU* 2.9 43.5 + - - +
552B VAL* 3.5 26.0 - - + -
553B PRO 3.9 16.8 - - - +
554B THR* 4.1 2.2 - - + -
558B MET* 3.8 23.8 - - + -
560B CYS* 5.4 0.9 - - + -
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Residues in contact with GLN 344 (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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137B TYR* 4.8 1.7 + - - -
149B ASP* 5.3 4.8 - - - +
165B TYR* 3.5 28.9 - - + +
340B ILE* 3.1 33.3 + - + +
341B VAL 3.2 4.2 + - - +
343B VAL* 1.3 87.4 - - - +
345B CYS* 1.3 63.2 + - - +
347B GLU* 4.1 12.3 + - - +
348B HIS* 3.1 24.4 + - - +
452B ARG* 6.3 0.2 - - - +
553B PRO 5.5 1.8 + - - -
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Residues in contact with CYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 3.9 36.9 + - - +
168B LEU* 3.9 25.6 - - + -
169B PHE* 4.2 12.8 - - - -
318B LEU* 5.1 5.2 - - - -
320B PHE* 5.6 1.1 - - - -
341B VAL 3.1 12.8 + - - +
342B LEU* 3.5 11.2 - - + +
344B GLN* 1.3 78.4 - - - +
346B THR* 1.3 65.9 + - - +
348B HIS* 3.3 4.5 + - - +
349B LEU* 3.0 37.9 + - - +
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Residues in contact with THR 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.8 5.1 - - + +
112B PHE* 4.6 14.1 - - + -
318B LEU* 6.1 0.2 - - + -
320B PHE* 5.1 6.5 - - + -
330B VAL* 4.4 22.2 - - + -
342B LEU* 2.9 35.9 + - + +
343B VAL* 3.0 14.2 + - - -
345B CYS* 1.3 78.4 - - + +
347B GLU* 1.3 57.1 + - - +
349B LEU* 3.2 9.5 + - - +
350B LEU* 2.8 34.5 + - - +
558B MET* 3.2 22.5 - - - +
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Residues in contact with GLU 347 (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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343B VAL* 2.9 28.3 + - - +
344B GLN* 4.1 14.0 + - - +
346B THR* 1.3 74.1 + - - +
348B HIS* 1.3 65.7 + - - +
350B LEU* 4.9 0.4 - - - -
351B LYS* 3.0 42.5 + - - +
554B THR* 3.3 15.7 - - - -
555B THR* 2.7 50.3 + - - +
556B MET* 3.9 22.1 + - - -
558B MET* 4.0 11.4 - - + -
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Residues in contact with HIS 348 (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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133B GLY 5.9 0.2 - - - -
136B SER* 5.9 1.6 - - - -
137B TYR* 3.3 41.1 - + + +
140B LEU* 3.7 23.4 - - + +
146B LEU* 5.1 6.3 - - + -
344B GLN 3.1 18.6 + - - +
345B CYS 3.5 4.5 - - - +
347B GLU* 1.3 76.8 - - - +
349B LEU* 1.3 64.2 + - + +
351B LYS* 4.0 5.3 - - - +
352B HIS* 3.2 58.8 + + - +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 5.0 5.6 - - + +
133B GLY* 3.1 42.2 - - - +
134B VAL* 3.7 25.6 - - + +
137B TYR* 3.8 13.7 - - + -
169B PHE* 5.4 1.6 - - + -
320B PHE* 3.8 24.0 - - + -
345B CYS* 3.0 31.5 + - - +
346B THR* 3.5 10.3 - - - +
347B GLU 3.2 0.2 - - - -
348B HIS* 1.3 77.3 - - - +
350B LEU* 1.3 67.1 + - + +
352B HIS* 3.2 14.0 + - + +
353B MET* 3.3 22.1 + - + +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.0 44.6 - - + -
115B GLN* 6.3 0.2 - - - +
126B PHE* 5.1 5.8 - - + -
130B LEU* 6.0 0.9 - - + -
346B THR 2.8 21.7 + - - +
347B GLU 4.0 1.1 - - - +
349B LEU* 1.3 73.3 - - + +
351B LYS* 1.3 64.1 + - - +
353B MET* 3.0 34.9 + - - +
354B MET* 3.7 8.7 - - - +
556B MET* 3.6 28.7 - - + -
557B GLU 5.7 1.3 - - - +
558B MET* 3.8 30.5 - - + -
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Residues in contact with LYS 351 (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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347B GLU* 3.0 30.6 + - - +
348B HIS* 4.0 6.3 - - - +
350B LEU* 1.3 76.0 - - - +
352B HIS* 1.3 64.5 + - + +
353B MET 3.2 0.2 - - - -
354B MET* 3.1 32.6 + - + +
355B THR* 3.5 10.2 + - - +
555B THR* 3.8 25.2 + - - +
556B MET* 4.1 20.9 - - + -
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Residues in contact with HIS 352 (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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129B CYS* 5.2 1.4 - - - -
133B GLY* 5.7 8.0 - - - -
136B SER* 5.6 7.3 - - - -
140B LEU* 5.7 1.8 - - + -
348B HIS* 3.2 49.2 + + - +
349B LEU* 3.2 7.0 + - + +
350B LEU 3.2 1.2 - - - -
351B LYS* 1.3 81.3 - - + +
353B MET* 1.3 58.0 + - - +
354B MET 3.1 5.7 + - - -
355B THR* 3.2 38.6 + - + +
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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