Contacts of the helix formed by residues 350 - 359 (chain A) in PDB entry 6AF6
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 GLY 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A ASP 3.4 7.0 + - - -
347A GLN* 3.5 9.9 + - - -
348A GLU 3.4 2.8 - - - -
349A LEU* 1.3 80.0 - - - +
351A LEU* 1.3 60.2 + - - +
352A VAL 3.4 2.0 - - - -
353A ARG* 3.8 12.8 - - - +
354A HIS* 2.9 28.8 + - - +
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Residues in contact with LEU 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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259A LEU* 3.8 28.0 - - + -
262A THR* 4.6 11.4 - - + -
333A GLY 5.1 0.9 - - - +
336A ALA* 4.4 7.4 - - + +
337A ILE* 4.0 18.7 - - + +
340A PHE* 3.3 57.7 - - + -
344A ALA* 4.1 18.1 + - + +
346A ASP 4.8 2.0 + - - -
349A LEU* 4.5 16.5 - - + +
350A GLY* 1.3 77.5 - - - +
352A VAL* 1.3 67.8 + - - +
354A HIS* 3.3 7.9 + - + +
355A LEU* 3.1 20.6 + - - +
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Residues in contact with VAL 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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337A ILE* 4.2 18.2 - - + -
344A ALA 3.6 21.0 + - - +
345A MET* 3.8 25.4 - - + -
346A ASP 5.6 1.1 + - - +
350A GLY 3.4 0.2 - - - -
351A LEU* 1.3 74.6 - - - +
353A ARG* 1.3 65.2 + - - +
355A LEU* 3.1 8.2 + - + +
356A LEU* 3.0 34.4 + - + +
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Residues in contact with ARG 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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32A ILE* 3.7 31.8 + - + +
35A LYS* 4.7 10.7 - - - +
204A ASP* 2.8 34.8 + - - +
207A SER* 3.5 20.8 + - - +
347A GLN* 6.0 0.9 - - - +
350A GLY* 3.6 15.5 + - - +
351A LEU 3.3 0.4 - - - -
352A VAL* 1.3 79.0 - - - +
354A HIS* 1.3 63.4 + - - +
356A LEU* 3.2 28.4 + - - +
357A ASN* 2.9 38.4 + - - +
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Residues in contact with HIS 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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83A ILE* 5.8 0.8 - - + +
255A GLY* 4.0 27.3 - - - -
256A LEU* 5.2 1.4 + - - -
259A LEU* 3.6 39.8 - - + +
329A ALA* 4.7 3.0 + - - +
333A GLY* 4.3 9.6 - - - -
350A GLY 2.9 18.9 + - - +
351A LEU* 3.5 9.9 - - + +
352A VAL 3.2 0.2 - - - -
353A ARG* 1.3 76.4 - - - +
355A LEU* 1.3 63.5 + - - +
357A ASN* 3.1 10.2 + - - +
358A MET* 3.0 60.4 + - + +
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Residues in contact with LEU 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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330A VAL* 3.5 42.8 - - + +
333A GLY* 4.3 5.4 - - - -
334A LEU* 3.7 32.3 - - + +
337A ILE* 3.9 18.4 - - + -
351A LEU 3.1 11.4 + - - +
352A VAL* 3.1 12.6 + - + +
354A HIS* 1.3 80.3 - - - +
356A LEU* 1.3 66.6 + - + +
358A MET* 3.0 13.4 + - + +
359A ILE* 3.1 25.7 + - + +
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Residues in contact with LEU 356 (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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204A ASP* 3.9 26.7 - - + +
205A CYS* 3.1 41.1 - - - +
352A VAL* 3.0 29.9 + - + +
353A ARG* 3.5 41.3 - - - +
355A LEU* 1.3 77.8 - - + +
357A ASN* 1.3 64.1 + - - +
359A ILE* 3.3 13.3 + - + -
360A PRO* 3.2 6.2 - - - +
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Residues in contact with ASN 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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81A ARG 4.8 4.4 + - - -
83A ILE* 2.9 37.0 - - + +
205A CYS* 4.5 0.5 - - - -
206A LEU* 2.9 42.6 + - + +
207A SER 4.4 1.6 + - - -
252A PHE* 4.2 7.4 - - - -
353A ARG* 2.9 38.5 + - - +
354A HIS* 3.1 11.9 + - - +
356A LEU* 1.3 77.7 - - - +
358A MET* 1.3 71.1 + - + +
360A PRO* 3.4 8.5 - - - +
361A SER 4.9 0.9 + - - -
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Residues in contact with MET 358 (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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83A ILE* 3.3 33.9 - - + -
252A PHE* 3.5 25.8 - - + +
255A GLY* 5.8 0.9 - - - -
256A LEU 6.0 0.2 - - - -
329A ALA* 3.8 31.6 - - + +
330A VAL* 3.6 18.0 - - + +
354A HIS* 3.0 49.4 + - + +
355A LEU* 3.0 9.2 + - - +
357A ASN* 1.3 90.7 - - + +
359A ILE* 1.3 64.6 + - - +
360A PRO 3.3 1.1 - - - -
361A SER* 2.7 29.3 + - - -
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Residues in contact with ILE 359 (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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205A CYS* 4.1 11.0 - - - -
330A VAL* 4.1 14.4 - - + -
355A LEU* 3.1 34.4 + - + +
356A LEU* 3.7 24.5 - - + +
358A MET* 1.3 76.9 - - - +
360A PRO* 1.3 70.5 - - + +
361A SER 3.1 1.4 + - - -
362A ARG* 3.4 26.1 + - - +
363A ILE* 4.3 12.9 - - + +
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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