Contacts of the helix formed by residues 346 - 357 (chain A) in PDB entry 6H7L
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 SER 346 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.2 2.1 - - - +
77A ASN* 5.5 0.3 + - - -
344A CYS 3.4 2.6 - - - -
345A ARG* 1.3 79.8 - - - +
347A PRO* 1.4 70.9 - - - +
348A ASP* 3.7 7.7 + - - +
349A PHE* 2.9 34.5 + - - -
350A ARG* 2.9 24.8 + - - +
105C TYR* 3.6 32.6 - - - -
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Residues in contact with PRO 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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345A ARG 3.6 0.6 - - - -
346A SER* 1.4 87.8 - - - +
348A ASP* 1.3 59.6 + - - +
350A ARG* 3.4 10.2 + - + +
351A LYS* 3.1 42.5 + - - +
105C TYR* 3.8 18.2 - - + -
106C ASP 5.3 3.1 - - - +
107C TYR* 4.0 31.6 - - + -
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Residues in contact with ASP 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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69A THR* 5.5 2.0 - - + +
71A ARG* 3.9 48.2 + - + +
72A LEU* 3.7 22.5 - - + +
346A SER* 3.2 5.1 - - - +
347A PRO* 1.3 79.3 - - - +
349A PHE* 1.3 64.4 + - - +
351A LYS* 3.5 19.7 + - - +
352A ALA* 3.1 23.6 + - - +
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Residues in contact with PHE 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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62A VAL* 4.2 4.9 - - + -
65A ALA* 4.1 8.5 - - + -
66A ILE* 3.6 40.2 - - + -
72A LEU* 3.7 17.7 - - + +
77A ASN* 3.5 28.7 - - - -
80A ILE* 4.6 1.6 - - + -
343A TYR 4.3 4.3 - - - -
344A CYS* 3.2 54.1 - - + +
346A SER* 2.9 29.8 + - - +
348A ASP* 1.3 73.5 - - - +
350A ARG* 1.3 64.1 + - - +
352A ALA* 3.2 2.4 + - - +
353A PHE* 2.9 50.6 + + + -
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Residues in contact with ARG 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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344A CYS 5.0 1.3 + - - -
345A ARG* 3.5 55.8 + - - +
346A SER 2.9 21.9 + - - +
347A PRO* 3.7 11.9 - - + +
349A PHE* 1.3 73.4 - - - +
351A LYS* 1.3 61.9 + - + +
353A PHE* 4.0 11.7 - - - +
354A LYS* 3.4 35.3 + - - +
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Residues in contact with LYS 351 (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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347A PRO* 3.1 30.5 + - - +
348A ASP* 3.8 19.3 + - - +
349A PHE 3.2 0.2 - - - -
350A ARG* 1.3 74.4 - - + +
352A ALA* 1.3 66.4 + - - +
354A LYS* 3.2 8.7 + - - +
355A ARG* 3.0 23.0 + - - +
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Residues in contact with ALA 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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65A ALA* 3.8 10.3 - - + -
69A THR* 3.7 16.6 - - + +
72A LEU* 3.6 24.7 - - + -
348A ASP 3.1 17.0 + - - +
349A PHE 3.2 3.5 + - - +
351A LYS* 1.3 77.9 - - - +
353A PHE* 1.3 57.2 + - - +
355A ARG* 3.3 13.9 + - - +
356A LEU* 2.8 35.4 + - - +
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Residues in contact with PHE 353 (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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61A LEU* 3.5 56.1 - - + -
62A VAL* 4.0 8.3 - - + -
65A ALA* 3.9 11.9 - - + -
340A PRO* 5.6 1.1 - - + -
344A CYS* 3.5 31.9 - - + -
349A PHE* 2.9 43.0 + + + +
350A ARG* 4.0 13.2 - - - +
352A ALA* 1.3 74.3 - - - +
354A LYS* 1.3 64.0 + - + +
356A LEU* 3.4 4.9 + - + +
357A LEU* 3.1 35.0 + - + +
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Residues in contact with LYS 354 (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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350A ARG* 3.4 20.1 + - - +
351A LYS* 3.2 10.8 + - - +
353A PHE* 1.3 76.8 - - + +
355A ARG* 1.3 65.3 + - - +
357A LEU* 3.1 22.9 + - - +
358A ALA 3.6 6.8 + - - -
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Residues in contact with ARG 355 (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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68A SER* 2.9 29.4 + - - -
69A THR* 2.7 31.6 + - - +
351A LYS 3.0 13.1 + - - +
352A ALA* 3.5 15.2 - - - +
354A LYS* 1.3 77.1 - - - +
356A LEU* 1.3 78.4 + - - +
358A ALA* 3.7 11.4 + - - -
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Residues in contact with LEU 356 (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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61A LEU* 3.5 24.9 - - + +
64A ALA* 3.6 14.4 - - + -
65A ALA* 3.5 31.4 - - + +
68A SER* 3.8 20.9 - - - +
352A ALA 2.8 26.5 + - - +
353A PHE* 3.8 7.6 - - + +
354A LYS 3.2 0.4 - - - -
355A ARG* 1.3 89.9 - - - +
357A LEU* 1.3 64.8 + - + +
358A ALA 3.3 4.1 + - - -
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Residues in contact with LEU 357 (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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61A LEU* 4.0 39.3 - - + -
353A PHE* 3.1 22.2 + - + +
354A LYS* 3.1 7.6 + - - +
356A LEU* 1.3 78.3 - - - +
358A ALA* 1.3 68.6 + - - +
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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