Contacts of the helix formed by residues 401 - 413 (chain A) in PDB entry 6S1M
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 PHE 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A ILE* 4.4 15.7 - - + -
319A CYS* 4.4 13.2 - - - -
326A PHE* 4.6 26.5 - + - -
327A PRO* 5.1 9.6 - - + -
397A ASN* 3.4 27.9 + - - +
398A ILE 4.0 0.2 - - - -
399A GLN 3.4 0.2 - - - -
400A ASN* 1.3 80.9 - - - +
402A ASP* 1.3 83.5 + - - +
403A LEU 3.8 0.7 - - - -
404A PRO* 4.0 4.1 - - - +
405A TYR* 3.2 51.7 + + - +
491A HIS* 6.5 1.1 - + - -
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Residues in contact with ASP 402 (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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315A PHE* 4.1 17.7 - - + +
316A ASP* 4.7 8.7 - - - +
317A ILE* 3.2 34.7 + - + +
396A TYR 4.1 4.7 - - - +
397A ASN 3.5 5.7 + - - +
398A ILE* 3.1 42.5 + - + +
401A PHE* 1.3 87.0 - - - +
403A LEU* 1.3 62.7 + - - +
405A TYR* 3.3 5.6 + - - +
406A LEU* 3.0 33.9 + - - +
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Residues in contact with LEU 403 (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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315A PHE* 4.1 24.7 - - + -
381A TRP* 4.8 10.3 - - + -
393A ILE* 5.9 5.8 - - + -
398A ILE* 3.1 23.0 + - + +
399A GLN* 5.1 2.2 - - - -
402A ASP* 1.3 80.2 - - - +
404A PRO* 1.3 62.6 - - + +
406A LEU* 3.2 13.7 + - + +
407A ILE* 3.0 36.0 + - + +
421A LEU* 6.3 0.9 - - + -
449A VAL* 4.3 20.9 - - + -
451A MET* 4.5 20.2 - - + -
456A GLN* 3.9 29.6 - - - +
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Residues in contact with PRO 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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329A PRO* 5.3 0.8 - - - +
398A ILE 4.2 0.2 - - - +
399A GLN 3.3 26.0 - - - +
400A ASN 4.4 2.5 - - - +
401A PHE 4.0 9.4 - - - +
402A ASP 3.9 0.7 - - - -
403A LEU* 1.3 87.8 - - + +
405A TYR* 1.3 59.5 + - - +
407A ILE* 3.9 1.3 - - + +
408A SER* 2.9 36.0 + - - +
431A ILE* 3.9 28.7 - - + -
447A LYS* 4.0 30.3 - - + +
449A VAL* 4.4 7.4 - - + -
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Residues in contact with TYR 405 (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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317A ILE* 4.5 8.3 - - + -
319A CYS* 3.8 17.6 - - - -
327A PRO* 4.2 11.3 - - + +
328A GLU 3.4 11.9 + - - -
329A PRO* 3.6 42.3 - - + +
332A ASP* 2.6 41.4 + - - +
334A VAL* 3.6 30.5 - - + -
401A PHE* 3.2 36.8 + + + +
402A ASP* 3.3 5.7 + - - +
403A LEU 3.3 0.8 - - - -
404A PRO* 1.3 76.6 - - - +
406A LEU* 1.3 58.1 + - - +
408A SER* 3.9 0.9 - - - -
409A ARG* 2.9 35.9 + - + +
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Residues in contact with LEU 406 (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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315A PHE* 4.2 21.8 - - + -
317A ILE* 4.5 11.4 - - + -
334A VAL* 4.5 22.2 - - + -
337A ILE* 4.5 13.0 - - + -
378A LEU* 3.8 24.9 - - + +
381A TRP* 4.3 18.6 - - + -
402A ASP 3.0 25.2 + - - +
403A LEU* 3.2 14.1 + - + +
405A TYR* 1.3 75.1 - - - +
407A ILE* 1.3 59.4 + - + +
409A ARG* 3.8 4.6 - - - +
410A ALA* 2.9 30.3 + - - +
418A PHE* 4.0 17.0 - - + -
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Residues in contact with ILE 407 (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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403A LEU* 3.0 21.6 + - + +
404A PRO* 3.9 4.7 - - + +
406A LEU* 1.3 77.3 - - - +
408A SER* 1.3 58.8 + - - +
410A ALA* 3.3 3.9 + - - +
411A GLN* 3.0 47.3 + - + +
418A PHE* 4.6 16.4 - - + -
419A PRO* 5.2 11.0 - - + -
421A LEU* 5.7 4.7 - - + -
429A SER* 4.7 22.0 - - - +
430A ASN* 5.9 0.4 - - - +
431A ILE* 3.9 28.0 - - + +
449A VAL* 3.7 31.4 - - + -
451A MET* 6.1 0.7 - - + -
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Residues in contact with SER 408 (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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329A PRO* 3.8 26.1 - - - +
330A GLU* 5.1 6.1 - - - -
404A PRO* 2.9 18.9 + - - +
407A ILE* 1.3 75.7 - - - +
409A ARG* 1.3 58.2 + - - +
411A GLN* 3.2 14.8 + - - +
412A THR* 3.0 32.8 + - - -
431A ILE* 4.3 11.1 - - - +
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Residues in contact with ARG 409 (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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329A PRO 3.6 23.6 + - - +
330A GLU* 3.7 21.0 + - - +
331A ARG* 3.9 7.7 + - - +
332A ASP 4.2 6.7 - - - +
333A PRO* 4.0 20.4 - - - +
334A VAL* 4.2 19.3 - - + -
374A GLU* 3.7 34.0 + - - +
378A LEU* 4.8 11.7 - - + -
405A TYR* 2.9 26.0 + - + +
406A LEU* 3.8 5.4 - - - +
408A SER* 1.3 77.1 - - - +
410A ALA* 1.3 60.6 + - - +
412A THR* 3.5 10.9 + - - +
413A LEU* 3.4 42.5 + - + +
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Residues in contact with ALA 410 (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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378A LEU* 4.4 15.6 - - + +
406A LEU 2.9 17.9 + - - +
407A ILE 3.8 3.8 - - - +
409A ARG* 1.3 75.7 - - - +
411A GLN* 1.3 63.1 + - - +
412A THR 3.5 0.3 + - - -
413A LEU* 3.6 2.2 + - - -
414A LYS* 3.6 4.5 + - - -
415A VAL* 3.5 32.2 + - + +
418A PHE* 3.6 37.0 - - + -
419A PRO* 5.6 1.6 - - + -
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Residues in contact with GLN 411 (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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407A ILE* 3.0 32.3 + - + +
408A SER* 3.2 14.5 + - - +
410A ALA* 1.3 78.2 - - - +
412A THR* 1.3 62.7 + - - +
413A LEU 3.6 0.2 + - - -
414A LYS* 3.8 9.8 + - - +
415A VAL 5.7 0.2 - - - -
419A PRO* 6.4 1.8 - - + -
429A SER 5.9 0.4 + - - -
430A ASN* 5.3 8.9 - - - +
431A ILE* 5.9 1.0 - - - +
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Residues in contact with THR 412 (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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329A PRO 4.0 10.8 + - - -
330A GLU* 4.2 23.5 + - + +
331A ARG* 5.7 3.8 - - - +
408A SER* 3.0 17.7 + - - -
409A ARG* 4.0 21.3 - - - +
410A ALA 3.3 0.4 - - - -
411A GLN* 1.3 78.7 - - - +
413A LEU* 1.3 64.4 + - + +
414A LYS* 3.5 14.7 + - - +
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Residues in contact with LEU 413 (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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374A GLU* 3.8 39.9 - - + +
375A GLU* 4.6 24.5 - - + +
378A LEU* 5.0 7.9 - - + -
409A ARG* 3.4 39.4 + - - +
410A ALA* 3.6 1.5 + - - +
411A GLN 3.4 0.4 - - - -
412A THR* 1.3 81.5 - - + +
414A LYS* 1.3 73.8 + - - +
415A VAL* 3.6 14.3 - - + +
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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