Contacts of the helix formed by residues 338 - 352 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TRP* 4.2 6.9 - - - -
95A TYR* 4.6 0.2 + - - -
164A GLN* 2.8 21.2 + - - +
334A HIS* 3.3 19.3 - - + -
337A PHE* 1.3 77.4 - - - +
339A GLY* 1.3 66.5 + - - +
340A ILE* 3.3 8.3 + - + +
341A VAL* 3.4 6.0 + - - +
342A LEU* 3.2 18.8 + - - +
458A ARG* 3.0 37.6 + - - +
459A VAL* 3.5 28.5 - - + +
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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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334A HIS* 4.6 7.5 + - - -
338A ASP* 1.3 72.3 - - - +
340A ILE* 1.3 60.1 + - - +
342A LEU* 3.5 12.4 - - - +
343A VAL* 2.9 37.6 + - - +
552A VAL* 5.0 15.3 - - - -
560A CYS* 5.7 5.4 - - - -
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Residues in contact with ILE 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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338A ASP* 3.3 6.3 + - + -
339A GLY* 1.3 76.3 - - - +
341A VAL* 1.3 64.4 + - + +
343A VAL* 3.4 3.9 + - - +
344A GLN* 3.1 43.5 + - + +
450A SER* 5.6 10.3 - - - -
452A ARG* 4.4 22.0 - - - +
551A GLN 4.3 18.6 - - - +
552A VAL* 5.1 3.6 - - + -
553A PRO* 4.4 16.8 - - + -
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Residues in contact with VAL 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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164A GLN* 3.7 33.0 + - + +
165A TYR* 3.7 62.2 - - + +
168A LEU* 4.4 11.9 - - + -
337A PHE* 4.7 3.1 - - + -
338A ASP 3.4 7.7 + - - +
339A GLY 3.3 0.4 - - - -
340A ILE* 1.3 74.6 - - + +
342A LEU* 1.3 66.7 + - - +
344A GLN* 3.2 2.6 + - - +
345A CYS* 3.1 21.7 + - - +
452A ARG* 4.2 19.3 - - - +
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Residues in contact with LEU 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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108A PRO* 5.5 6.1 - - + +
110A VAL* 3.6 28.5 - - + -
168A LEU* 4.9 3.6 - - + -
318A LEU* 3.6 31.9 - - + -
330A VAL* 4.9 6.3 - - + +
332A CYS* 3.8 22.2 - - + -
337A PHE* 4.2 15.9 - - + -
338A ASP 3.2 12.1 + - - +
339A GLY* 3.3 13.2 + - - +
341A VAL* 1.3 79.2 - - - +
343A VAL* 1.3 58.3 + - + +
345A CYS* 3.2 9.0 + - + +
346A THR* 2.9 47.8 + - + +
560A CYS* 5.7 2.7 - - - -
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Residues in contact with VAL 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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110A VAL* 4.8 12.6 - - + -
339A GLY* 2.9 20.3 + - - +
340A ILE* 3.8 5.2 - - - +
342A LEU* 1.3 76.0 - - + +
344A GLN* 1.3 68.5 + - - +
346A THR* 3.0 6.9 + - - +
347A GLU* 2.9 44.8 + - - +
552A VAL* 3.5 26.5 - - + -
553A PRO 3.9 16.4 - - - +
554A THR* 4.2 2.7 - - + -
558A MET* 3.8 24.0 - - + -
560A CYS* 5.4 0.4 - - + -
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Residues in contact with GLN 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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137A TYR* 4.8 1.7 + - - -
149A ASP* 5.3 5.0 - - - +
165A TYR* 3.5 29.6 - - + +
340A ILE* 3.1 33.1 + - + +
341A VAL 3.2 4.0 + - - +
343A VAL* 1.3 87.4 - - - +
345A CYS* 1.3 62.6 + - - +
347A GLU* 4.0 12.9 + - - +
348A HIS* 3.1 24.4 + - - +
553A PRO 5.5 1.8 + - - -
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Residues in contact with CYS 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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137A TYR* 3.9 35.5 + - - +
168A LEU* 3.9 25.1 - - + -
169A PHE* 4.2 13.2 - - - -
318A LEU* 5.1 4.9 - - - -
320A PHE* 5.6 1.1 - - - -
341A VAL 3.1 13.2 + - - +
342A LEU* 3.5 11.0 - - + +
344A GLN* 1.3 77.2 - - - +
346A THR* 1.3 67.6 + - - +
348A HIS* 3.3 4.3 + - - +
349A LEU* 3.0 39.1 + - - +
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Residues in contact with THR 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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110A VAL* 4.8 5.1 - - + +
112A PHE* 4.6 11.4 - - + -
318A LEU* 6.2 0.2 - - + -
320A PHE* 5.1 6.5 - - + -
330A VAL* 4.3 22.2 - - + -
342A LEU* 2.9 35.5 + - + +
343A VAL* 3.0 14.7 + - - +
345A CYS* 1.3 78.8 - - + +
347A GLU* 1.3 56.6 + - - +
349A LEU* 3.2 8.6 + - - +
350A LEU* 2.8 34.7 + - - +
558A MET* 3.2 24.6 - - - +
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Residues in contact with GLU 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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343A VAL* 2.9 27.8 + - - +
344A GLN* 4.0 14.1 + - - +
346A THR* 1.3 73.9 + - - +
348A HIS* 1.3 65.6 + - - +
350A LEU* 4.6 0.7 - - - -
351A LYS* 2.9 42.4 + - - +
554A THR* 3.3 15.8 - - - -
555A THR* 2.7 50.6 + - - +
556A MET* 3.9 22.3 + - - +
558A MET* 4.0 11.0 - - + -
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Residues in contact with HIS 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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133A GLY 5.9 0.4 - - - -
136A SER* 5.9 1.3 - - - -
137A TYR* 3.3 41.5 - + + +
140A LEU* 3.7 24.0 - - + +
146A LEU* 5.1 6.1 - - + -
344A GLN 3.1 19.2 + - - +
345A CYS 3.6 4.5 - - - +
347A GLU* 1.3 76.0 - - - +
349A LEU* 1.3 63.7 + - - +
351A LYS* 4.0 5.9 - - - +
352A HIS* 3.2 59.0 + + - +
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Residues in contact with LEU 349 (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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130A LEU* 5.0 6.1 - - + +
133A GLY* 3.1 41.0 - - - +
134A VAL* 3.7 25.1 - - + +
137A TYR* 3.8 15.5 - - + -
169A PHE* 5.4 1.3 - - + -
320A PHE* 3.8 25.1 - - + -
345A CYS* 3.0 30.7 + - - +
346A THR* 3.5 9.9 - - - +
348A HIS* 1.3 76.9 - - - +
350A LEU* 1.3 67.5 + - + +
352A HIS* 3.2 13.4 + - - +
353A MET* 3.3 22.5 + - - +
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Residues in contact with LEU 350 (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 PHE* 4.0 44.0 - - + -
115A GLN* 6.3 0.2 - - - +
126A PHE* 5.1 5.8 - - + -
130A LEU* 5.9 0.4 - - + -
346A THR 2.8 22.3 + - - +
347A GLU 4.0 1.3 - - - +
349A LEU* 1.3 73.7 - - + +
351A LYS* 1.3 63.3 + - - +
353A MET* 3.0 36.3 + - + +
354A MET* 3.7 9.3 - - - +
556A MET* 3.6 28.7 - - + -
557A GLU 5.7 1.1 - - - +
558A MET* 3.8 29.8 - - + -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A GLU* 2.9 28.9 + - - +
348A HIS* 4.0 6.3 - - - +
350A LEU* 1.3 75.1 - - - +
352A HIS* 1.3 65.2 + - + +
353A MET 3.2 0.2 - - - -
354A MET* 3.1 32.2 + - + +
355A THR* 3.5 9.9 + - - +
555A THR* 3.8 24.3 + - - +
556A MET* 4.1 21.3 - - + -
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Residues in contact with HIS 352 (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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129A CYS* 5.2 1.0 - - - -
133A GLY* 5.7 9.0 - - - -
136A SER* 5.6 7.5 - - - -
140A LEU* 5.7 2.0 - - + -
348A HIS* 3.2 46.9 + + - +
349A LEU* 3.2 7.0 + - - +
350A LEU 3.2 1.0 - - - -
351A LYS* 1.3 81.2 - - + +
353A MET* 1.3 57.2 + - - +
354A MET 3.1 6.1 + - - -
355A THR* 3.2 38.1 + - + +
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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