Contacts of the helix formed by residues 321 - 332 (chain C) in PDB entry 3COG
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 THR 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C ILE* 4.5 0.3 - - - +
320C GLY* 1.3 79.4 - - - +
322C LEU* 1.3 66.0 + - - +
323C GLN* 3.1 24.4 + - - +
324C HIS* 2.9 34.0 + - + +
325C ALA 3.2 8.8 + - - -
372C THR* 3.6 13.0 - - - +
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C THR* 1.3 74.9 - - - +
323C GLN* 1.3 59.1 + - + +
325C ALA* 3.3 1.6 + - + +
326C GLU* 2.9 50.5 + - - +
350C LEU* 3.4 33.7 - - + -
353C ILE* 4.1 11.9 - - + -
371C ASP* 3.5 43.8 - - + +
372C THR* 3.9 3.8 - - - +
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Residues in contact with GLN 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C THR* 3.1 13.7 + - - +
322C LEU* 1.3 77.9 - - + +
324C HIS* 1.3 62.3 + - + +
326C GLU* 3.4 13.2 + - - +
327C ILE* 3.0 38.7 + - + +
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Residues in contact with HIS 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 3.8 7.2 - - + -
319C LYS 3.7 14.1 - - - +
320C GLY* 3.4 9.3 - - - -
321C THR* 2.9 44.4 + - + +
323C GLN* 1.3 78.7 - - + +
325C ALA* 1.3 59.0 + - - +
327C ILE* 3.2 8.8 + - + +
328C PHE* 2.9 30.1 + - - +
397C ALA* 3.5 23.6 - - + +
398C HIS 4.7 0.2 - - - -
399C PRO* 3.6 25.5 - - + +
400C PRO* 3.7 17.1 - - + +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ILE* 3.9 25.1 - - + +
321C THR 3.2 7.4 + - - +
322C LEU* 3.5 9.6 - - + +
324C HIS* 1.3 74.4 - - - +
326C GLU* 1.3 57.9 + - - +
328C PHE* 3.4 2.4 + - - +
329C LEU* 2.9 35.6 + - - +
350C LEU* 4.0 16.4 - - + -
371C ASP 3.8 21.1 - - - +
372C THR* 4.7 0.2 - - - -
374C ILE* 4.2 8.5 - - + -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322C LEU* 2.9 49.7 + - + +
323C GLN* 3.7 14.1 - - - +
325C ALA* 1.3 75.0 - - - +
327C ILE* 1.3 60.6 + - - +
329C LEU* 3.3 6.5 + - - +
330C LYS* 3.0 41.2 + - - +
350C LEU* 4.7 0.9 - - + -
353C ILE* 4.5 8.7 - - - +
52D PRO* 4.4 26.2 - - + +
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C GLN* 3.0 29.4 + - + +
324C HIS* 3.8 11.0 - - + +
326C GLU* 1.3 72.8 - - - +
328C PHE* 1.3 67.1 + - - +
330C LYS* 3.4 24.1 + - - +
331C ASN* 2.8 44.6 + - - +
396C ALA* 3.6 23.8 - - + +
397C ALA* 3.7 14.8 - - - +
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C PHE* 4.0 20.4 - + - -
318C ILE* 3.7 14.8 - - + -
324C HIS 2.9 17.7 + - - +
325C ALA 3.5 2.2 - - - +
327C ILE* 1.3 79.1 - - - +
329C LEU* 1.3 87.4 + - + +
331C ASN 3.2 6.9 + - - -
332C LEU* 3.4 23.5 + - + +
374C ILE* 3.8 19.5 - - + -
376C LEU* 4.7 3.4 - - + -
390C LEU* 3.7 28.5 - - + -
393C ALA* 3.5 41.4 - - + +
394C LEU* 3.7 32.8 - - + -
397C ALA* 3.9 3.3 - - + +
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Residues in contact with LEU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C ALA 2.9 23.4 + - - +
326C GLU* 3.8 3.8 - - - +
328C PHE* 1.3 92.8 - - + +
330C LYS* 1.3 62.2 + - - +
332C LEU* 3.4 23.5 + - + +
337C LEU* 4.2 33.6 - - + +
348C ALA* 3.8 29.2 - - + -
349C GLU 4.4 4.3 - - - +
350C LEU* 4.0 28.7 - - + +
374C ILE* 4.4 7.9 - - + -
52D PRO* 3.9 27.4 - - + -
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Residues in contact with LYS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C GLU* 3.0 26.8 + - - +
327C ILE* 3.6 40.0 - - - +
328C PHE 3.3 0.2 - - - -
329C LEU* 1.3 77.9 - - - +
331C ASN* 1.3 69.7 + - - +
332C LEU 3.7 4.6 + - - +
337C LEU* 6.2 1.3 - - - -
50D GLY 5.4 8.1 - - - +
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Residues in contact with ASN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ILE* 2.8 42.8 + - - +
328C PHE 3.2 4.9 + - - +
330C LYS* 1.3 90.0 - - - +
332C LEU* 1.3 62.8 + - - +
333C LYS* 3.5 11.6 + - - +
392C GLN* 2.8 25.4 + - - +
393C ALA* 4.1 9.2 - - - -
396C ALA* 3.4 26.7 - - + +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C PHE* 3.4 26.9 + - + +
329C LEU* 3.4 26.3 + - + +
330C LYS 4.2 5.2 - - - +
331C ASN* 1.3 78.6 - - - +
333C LYS* 1.3 62.5 + - - +
334C LEU 3.8 0.2 - - - -
335C PHE* 3.7 25.1 - - + +
337C LEU* 5.6 3.1 - - - +
348C ALA* 3.7 29.8 - - + -
389C ASP* 3.5 22.4 - - - +
390C LEU* 4.1 11.0 - - + -
392C GLN* 4.0 0.2 - - - +
393C ALA* 3.6 20.4 - - + -
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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