Contacts of the helix formed by residues 346 - 357 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B LEU* 4.3 1.9 - - - +
77B ASN* 5.5 0.5 + - - -
344B CYS 3.4 2.8 - - - -
345B ARG* 1.3 80.0 - - - +
347B PRO* 1.3 69.8 - - - +
348B ASP* 3.7 8.3 + - - +
349B PHE* 2.9 33.7 + - - +
350B ARG* 2.9 24.9 + - - +
105D TYR* 3.6 35.0 - - - -
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Residues in contact with PRO 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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345B ARG 3.6 1.0 - - - +
346B SER* 1.3 88.3 - - - +
348B ASP* 1.3 59.5 + - - +
350B ARG* 3.4 15.2 + - - +
351B LYS* 3.1 45.3 + - - +
105D TYR* 3.8 20.9 - - + -
106D ASP 5.4 3.4 - - - +
107D TYR* 4.2 27.6 - - + -
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Residues in contact with ASP 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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69B THR* 5.5 2.1 - - + +
71B ARG* 3.3 47.1 + - + +
72B LEU* 3.7 22.0 - - + +
346B SER* 3.2 5.5 - - - +
347B PRO* 1.3 80.1 - - - +
349B PHE* 1.3 61.8 + - - +
351B LYS* 3.5 20.5 + - - +
352B ALA* 3.1 23.7 + - - +
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Residues in contact with PHE 349 (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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62B VAL* 4.2 4.3 - - + -
65B ALA* 4.1 7.0 - - + -
66B ILE* 3.6 39.9 - - + -
72B LEU* 3.7 17.7 - - + +
77B ASN* 3.5 29.2 - - - -
80B ILE* 4.6 2.0 - - + -
343B TYR 4.3 3.4 - - - -
344B CYS* 3.2 54.3 - - + +
346B SER* 2.9 29.6 + - - +
348B ASP* 1.3 74.4 - - - +
350B ARG* 1.3 58.1 + - - +
352B ALA* 3.2 2.1 + - - +
353B PHE* 2.9 57.0 + + + -
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Residues in contact with ARG 350 (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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344B CYS 5.4 0.9 - - - +
345B ARG* 3.2 57.5 + - - +
346B SER 2.9 17.8 + - - +
347B PRO* 3.7 15.2 - - + +
349B PHE* 1.3 72.1 - - + +
351B LYS* 1.3 61.3 + - + +
353B PHE* 3.8 9.6 + - + +
354B LYS* 3.4 30.0 + - - +
105D TYR* 5.5 2.2 + - - -
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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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71B ARG* 5.9 1.6 - - - +
347B PRO* 3.1 31.2 + - - +
348B ASP* 3.8 21.0 + - - +
349B PHE 3.2 0.2 - - - -
350B ARG* 1.3 75.2 - - + +
352B ALA* 1.3 64.9 + - - +
354B LYS* 3.2 8.3 + - - +
355B ARG* 3.0 23.6 + - - +
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Residues in contact with ALA 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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65B ALA* 3.9 10.5 - - + -
69B THR* 3.7 16.2 - - + +
72B LEU* 3.6 24.9 - - + -
348B ASP 3.1 15.1 + - - +
349B PHE 3.2 3.6 + - - +
351B LYS* 1.3 78.1 - - - +
353B PHE* 1.3 57.9 + - - +
355B ARG* 3.3 12.8 + - - +
356B LEU* 2.8 35.1 + - - +
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Residues in contact with PHE 353 (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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61B LEU* 3.5 49.6 - - + -
62B VAL* 4.0 8.7 - - + -
65B ALA* 3.9 12.1 - - + -
340B PRO* 5.6 1.6 - - + -
344B CYS* 3.5 31.6 - - + -
349B PHE* 2.9 42.6 + + + +
350B ARG* 4.1 9.2 - - + +
352B ALA* 1.3 73.5 - - - +
354B LYS* 1.3 65.7 + - + +
356B LEU* 3.4 5.0 + - + +
357B LEU* 3.1 38.9 + - + +
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Residues in contact with LYS 354 (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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350B ARG* 3.4 16.5 + - - +
351B LYS* 3.2 10.6 + - - +
353B PHE* 1.3 74.1 - - + +
355B ARG* 1.3 66.7 + - - +
357B LEU* 3.1 16.4 + - - -
358B ALA* 3.5 12.3 + - - +
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Residues in contact with ARG 355 (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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179A MET 4.9 6.3 + - - +
180A HIS* 4.7 14.1 + - - +
181A TRP* 5.7 0.2 - - - -
183A ARG* 6.2 0.6 - - - +
185A GLU* 5.7 2.6 + - - -
68B SER* 2.9 30.8 + - - -
69B THR* 2.7 32.3 + - - +
351B LYS 3.0 14.1 + - - +
352B ALA* 3.5 14.0 - - - +
354B LYS* 1.3 77.0 - - - +
356B LEU* 1.3 77.9 + - - +
358B ALA* 3.2 21.1 - - + +
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Residues in contact with LEU 356 (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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179A MET* 3.2 15.1 - - - +
181A TRP* 2.9 61.7 + - + +
61B LEU* 3.5 25.1 - - + +
64B ALA* 3.6 10.1 - - + -
65B ALA* 3.5 33.0 - - + +
68B SER* 3.8 20.2 - - - +
352B ALA 2.8 25.9 + - - +
353B PHE* 3.8 8.5 - - + +
354B LYS 3.2 0.4 - - - -
355B ARG* 1.3 86.2 - - - +
357B LEU* 1.3 57.8 + - - +
358B ALA 3.3 1.1 - - - -
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Residues in contact with LEU 357 (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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179A MET* 4.1 7.9 - - + -
181A TRP* 5.0 4.5 - - + -
61B LEU* 4.0 41.3 - - + -
353B PHE* 3.1 23.4 + - + +
354B LYS* 3.1 6.7 + - - +
356B LEU* 1.3 77.2 - - - +
358B ALA* 1.3 63.8 + - - +
359B PHE 5.1 0.3 - - - -
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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