Contacts of the helix formed by residues 326 - 333 (chain F) in PDB entry 2QC8
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 PRO 326 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255F ASN* 5.1 0.2 - - - +
316F VAL* 4.2 0.7 - - - +
324F ARG* 3.4 32.3 - - - +
325F ILE* 1.3 89.7 - - + +
327F ARG* 1.3 66.0 + - - +
328F THR* 4.4 7.4 - - - +
329F VAL* 3.2 11.1 + - + +
330F GLY* 3.1 16.6 + - - -
336F TYR* 3.8 46.9 - - + +
337F PHE* 4.5 1.6 - - - -
338F GLU* 4.6 4.5 - - + +
61J ASN* 6.2 0.7 - - - +
76J ASP* 3.8 10.8 - - - +
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Residues in contact with ARG 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F VAL* 4.2 17.1 - - + +
317F ALA* 3.5 18.6 - - + +
325F ILE 3.8 0.8 + - - -
326F PRO* 1.3 69.5 - - - +
328F THR* 1.3 65.8 + - - +
330F GLY* 2.9 3.8 + - - -
331F GLN* 2.9 38.1 + - - +
61J ASN* 6.4 0.9 - - - -
74J ASN* 3.0 31.3 + - - +
76J ASP* 3.0 54.3 + - + +
78J TYR* 3.4 40.3 - - + +
104J TYR* 3.6 31.2 + - - +
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Residues in contact with THR 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F PRO* 3.4 6.3 - - - +
327F ARG* 1.3 76.2 - - - +
329F VAL* 1.3 59.6 + - + +
331F GLN* 3.4 6.2 + - - +
332F GLU* 2.8 64.4 + - - +
336F TYR* 6.0 2.7 - - + -
61J ASN* 4.4 13.5 + - - -
78J TYR* 5.7 7.3 - - - -
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Residues in contact with VAL 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F LEU* 4.3 4.4 - - + +
270F ILE* 3.6 17.5 - - + -
325F ILE* 3.6 20.0 - - + -
326F PRO* 3.2 17.6 + - + +
327F ARG 3.2 0.8 - - - -
328F THR* 1.3 78.1 - - + +
330F GLY* 1.3 60.0 + - - +
333F LYS* 2.9 27.4 + - - -
334F LYS 3.3 25.7 + - - +
335F GLY* 4.3 0.9 - - - -
336F TYR* 3.3 47.6 - - + +
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Residues in contact with GLY 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F LEU* 4.3 12.2 - - - +
316F VAL* 4.9 14.4 - - - -
325F ILE* 4.2 6.1 - - - +
326F PRO 3.1 9.6 + - - -
327F ARG 2.9 8.1 + - - -
329F VAL* 1.3 76.4 - - - +
331F GLN* 1.3 66.7 + - - +
333F LYS* 3.4 15.6 + - - +
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Residues in contact with GLN 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327F ARG* 2.9 33.9 + - - +
328F THR* 3.6 8.7 - - - +
330F GLY* 1.3 73.5 - - - +
332F GLU* 1.3 67.4 + - + +
333F LYS* 3.3 11.3 + - - +
78J TYR* 3.7 20.9 + - + +
104J TYR 5.4 2.8 + - - -
106J ARG* 5.6 7.8 + - - +
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F GLU* 4.6 6.2 - - - +
328F THR* 2.8 44.6 + - + +
331F GLN* 1.3 76.7 - - + +
333F LYS* 1.3 69.4 + - - +
334F LYS* 3.1 39.2 + - + +
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Residues in contact with LYS 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F ASN* 3.1 32.6 - - - +
266F GLY 3.1 9.2 + - - -
267F LEU* 3.0 39.3 + - + +
329F VAL 2.9 12.2 + - - -
330F GLY 3.8 11.4 - - - +
331F GLN 3.2 9.4 - - - +
332F GLU* 1.3 76.5 - - - +
334F LYS* 1.3 57.0 + - - +
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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