Contacts of the helix formed by residues 398 - 412 (chain A) in PDB entry 6PUO
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 ARG 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A PRO* 4.4 9.3 - - - +
383A LEU* 6.5 0.2 - - + -
394A PHE* 3.7 30.0 - - + -
395A THR* 3.6 30.5 - - + +
397A SER* 1.3 80.2 + - - +
399A ILE* 1.3 67.6 + - + +
400A VAL 3.2 1.8 - - - -
401A GLU* 3.2 10.2 + - + +
402A TRP* 3.0 72.8 + - + +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 3.8 25.1 - - + -
379A ILE* 4.4 10.6 - - + +
380A GLN* 4.8 17.3 - - + -
383A LEU* 4.5 26.9 - - + -
394A PHE* 5.2 2.5 - - + -
395A THR 3.8 11.7 - - - +
396A GLU* 3.3 34.3 - - + +
398A ARG* 1.3 78.9 - - + +
400A VAL* 1.3 59.9 + - - +
402A TRP* 3.7 9.3 - - + +
403A THR* 2.9 33.6 + - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 5.1 9.6 - - + -
396A GLU 3.9 7.2 - - - +
397A SER* 3.3 28.7 - - - +
399A ILE* 1.3 79.9 - - + +
401A GLU* 1.3 64.8 + - - +
403A THR* 2.4 23.3 + - - -
404A LYS* 3.0 11.6 + - - +
1255A PHE* 4.9 7.4 - - + -
1256A PRO* 3.5 31.0 - - + +
1258A PRO* 3.7 17.1 - - + +
1268A PHE* 4.2 19.7 - - + -
1270A ILE* 6.0 7.6 - - + -
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A SER 4.8 2.2 - - - +
398A ARG* 3.2 18.0 + - + +
400A VAL* 1.3 80.6 - - - +
402A TRP* 1.3 69.8 + - + +
404A LYS* 3.2 5.1 + - - +
405A LYS* 2.9 64.2 + - + +
1245A LEU* 4.7 10.2 - - - +
1256A PRO* 3.3 35.8 - - + +
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Residues in contact with TRP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO* 3.6 36.2 + - + -
337A LEU* 5.1 18.8 - - + +
359A VAL* 5.5 5.8 - - + -
379A ILE* 3.9 15.3 - - + -
383A LEU* 3.6 30.7 - - + -
387A PHE* 4.5 16.6 - + - -
394A PHE* 4.2 17.5 - + - -
398A ARG* 3.0 63.1 + - + +
399A ILE* 3.3 8.9 + - + +
400A VAL 3.2 0.4 - - - -
401A GLU* 1.3 87.1 - - + +
403A THR* 1.3 61.1 + - - +
405A LYS* 3.8 6.1 - - + +
406A ILE* 2.9 38.8 + - + +
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Residues in contact with THR 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ILE* 5.1 7.1 - - + +
375A THR* 4.5 3.1 - - - +
376A ILE* 3.9 24.4 - - + +
379A ILE* 3.6 31.2 - - + -
399A ILE 2.9 15.6 + - - +
400A VAL* 2.4 27.2 + - - -
402A TRP* 1.3 73.3 - - - +
404A LYS* 1.3 56.5 + - - -
406A ILE* 4.2 1.9 - - - +
407A GLN* 2.9 42.5 + - - +
1258A PRO* 3.3 21.2 - - - +
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Residues in contact with LYS 404 (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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400A VAL 3.0 9.2 + - - +
401A GLU* 3.2 9.8 + - - +
403A THR* 1.3 80.9 + - - +
405A LYS* 1.3 62.0 + - + +
407A GLN* 3.9 8.6 - - - +
408A ASP* 3.0 64.3 + - - +
1243A ARG* 2.7 41.2 + - - +
1245A LEU* 4.5 15.7 - - + +
1254A ARG* 5.6 1.0 - - - +
1255A PHE 5.3 1.6 + - - -
1256A PRO* 3.9 22.5 - - + +
1257A VAL* 3.4 31.8 + - - +
1258A PRO* 4.5 3.8 - - + -
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.7 24.3 - - + +
338A HIS* 3.3 45.9 + - - +
341A ASP* 3.9 27.8 + - + +
401A GLU* 2.9 45.6 + - + +
402A TRP* 3.8 3.4 - - + +
404A LYS* 1.3 79.8 - - + +
406A ILE* 1.3 58.3 + - - +
408A ASP* 3.3 7.0 + - + +
409A ILE* 2.9 33.7 + - + +
1245A LEU* 4.6 15.5 - - + -
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Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.9 26.0 - - + -
362A VAL* 4.4 16.2 - - + -
363A ILE* 3.8 20.4 - - + -
366A VAL* 3.9 26.9 - - + -
374A ILE* 4.3 14.4 - - + -
379A ILE* 3.8 24.2 - - + -
402A TRP* 2.9 19.5 + - + +
403A THR* 4.2 3.6 - - - +
405A LYS* 1.3 75.5 - - - +
407A GLN* 1.3 58.5 + - + +
409A ILE* 3.7 5.6 - - + +
410A VAL* 2.9 34.2 + - + +
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Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 4.7 8.5 - - + +
372A SER* 4.3 3.3 - - - +
374A ILE* 3.4 45.6 - - + +
403A THR* 2.9 23.3 + - - +
404A LYS* 3.9 6.8 - - - +
406A ILE* 1.3 77.5 - - - +
408A ASP* 1.3 58.2 + - - +
410A VAL* 3.9 0.8 - - - -
411A ARG* 3.0 39.0 + - - +
1243A ARG* 4.2 4.8 - - - +
1258A PRO* 3.9 11.9 - - - +
1259A ASN* 3.2 57.1 + - - +
1260A GLU 5.1 0.2 + - - -
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Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP* 4.3 7.8 - - - +
404A LYS* 3.0 50.9 + - - +
405A LYS* 3.3 7.5 + - + +
407A GLN* 1.3 77.5 - - - +
409A ILE* 1.3 61.3 + - - +
411A ARG* 2.9 29.7 + - - +
412A ARG* 3.2 40.4 + - - +
1243A ARG 5.0 0.9 - - - +
1244A HIS* 5.0 9.7 + - - -
1245A LEU* 5.0 4.5 + - - +
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Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 4.1 17.0 - - + +
340A ILE* 3.7 28.0 - - + -
341A ASP* 3.9 30.5 - - + +
344A THR* 4.6 12.4 - - + +
363A ILE* 4.7 13.7 - - + -
405A LYS 2.9 21.7 + - - +
406A ILE* 3.7 6.7 - - - +
407A GLN 3.2 0.2 - - - -
408A ASP* 1.3 75.6 - - - +
410A VAL* 1.3 66.2 + - + +
411A ARG 3.1 4.9 + - - -
412A ARG* 3.3 22.7 + - - +
416A LEU* 3.8 30.7 - - + +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 4.7 4.9 - - + -
366A VAL* 3.8 23.6 - - + +
367A ALA* 3.6 27.4 - - - +
369A LEU 4.3 9.2 - - - +
370A PRO 6.1 0.9 - - - -
371A VAL* 5.8 2.8 - - - +
374A ILE* 5.0 9.0 - - + -
406A ILE* 2.9 29.8 + - + +
407A GLN 3.9 1.1 - - - +
409A ILE* 1.3 77.7 - - + +
411A ARG* 1.3 65.5 + - - +
412A ARG 4.2 0.8 - - - -
413A ARG* 4.1 10.7 + - - +
416A LEU* 4.2 18.6 - - + -
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 3.4 36.7 - - + +
407A GLN* 3.0 29.4 + - - +
408A ASP* 2.9 37.1 + - - +
409A ILE 3.1 0.2 - - - -
410A VAL* 1.3 78.6 - - - +
412A ARG* 1.3 64.2 + - + +
413A ARG* 3.0 10.0 + - - +
1240A VAL* 3.4 43.1 - - - +
1243A ARG* 3.5 14.8 - - - +
1259A ASN* 3.9 4.8 + - - +
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Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP* 4.0 8.5 + - - -
344A THR* 3.3 49.4 + - - +
345A THR* 3.4 29.6 - - - +
408A ASP* 3.2 33.3 + - - +
409A ILE 3.3 15.0 + - - +
410A VAL 4.2 0.8 - - - -
411A ARG* 1.3 80.3 - - + +
413A ARG* 1.3 61.3 + - - +
414A GLN* 3.1 8.0 + - + +
415A LEU* 5.0 14.4 - - + -
416A LEU* 3.9 17.0 + - - +
1244A HIS* 5.1 9.1 + - - -
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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
------------------------------------------------------------
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