Contacts of the helix formed by residues 324 - 334 (chain C) in PDB entry 3CLP
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 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C GLY 5.1 0.9 - - - -
270C ASP* 3.0 26.0 + - - +
301C LEU* 3.7 23.8 - - - -
323C HIS* 1.3 72.9 - - - +
325C ALA* 1.3 63.5 + - - +
327C PHE* 3.3 12.2 + - - +
328C GLN* 3.1 27.3 + - - +
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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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323C HIS* 3.2 5.2 - - + +
324C SER* 1.3 81.7 + - - +
326C ASP* 1.3 66.8 + - - +
328C GLN* 3.5 10.8 + - - +
329C MET* 3.3 18.5 + - - +
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Residues in contact with ASP 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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250C ALA* 3.4 29.5 - - + +
322C LEU* 3.7 23.1 - - + +
323C HIS* 3.0 22.9 + - - +
325C ALA* 1.3 79.6 - - - +
327C PHE* 1.3 59.6 + - - +
329C MET* 3.3 22.2 + - + +
330C LEU* 2.9 28.9 + - - +
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Residues in contact with PHE 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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272C MET* 3.4 30.1 - - + -
298C GLU* 4.6 3.1 - - + -
301C LEU* 3.6 38.4 - - + -
302C ILE* 3.5 36.8 - - + -
322C LEU* 4.1 13.6 - - + +
323C HIS 2.9 12.7 + - - +
324C SER 3.3 12.5 + - - +
326C ASP* 1.3 74.4 - - - +
328C GLN* 1.3 74.1 + - - +
330C LEU* 3.3 3.1 + - + +
331C CYS* 3.0 43.8 + - - -
341C PHE* 3.4 31.0 - + - -
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Residues in contact with GLN 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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301C LEU 5.7 3.0 + - - -
324C SER 3.1 14.6 + - - +
325C ALA* 3.5 11.7 - - - +
326C ASP 3.3 0.2 - - - -
327C PHE* 1.3 96.2 - - + +
329C MET* 1.3 60.3 + - - +
331C CYS* 3.4 8.9 + - - +
332C SER* 3.0 30.2 + - - +
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Residues in contact with MET 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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246C GLU* 3.9 38.4 - - + +
247C ILE* 3.7 27.4 - - + -
250C ALA* 4.6 1.6 - - + -
325C ALA 3.3 11.0 + - - +
326C ASP* 3.5 31.2 - - + +
327C PHE 3.3 0.2 - - - -
328C GLN* 1.3 79.0 - - - +
330C LEU* 1.3 56.5 + - - +
332C SER* 3.4 5.4 + - - -
333C SER* 2.9 43.1 + - - +
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Residues in contact with LEU 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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236C PHE* 4.3 8.5 - - + -
239C LEU* 4.2 11.4 - - + -
243C VAL* 5.3 0.9 - - + -
247C ILE* 3.8 30.3 - - + +
274C PHE* 4.3 8.3 - - + -
322C LEU* 3.8 21.3 - - + -
326C ASP 2.9 17.4 + - - +
327C PHE* 3.5 5.6 - - + +
329C MET* 1.3 76.6 - - - +
331C CYS* 1.3 57.4 + - - +
333C SER* 3.3 2.7 + - - -
334C SER* 2.8 28.4 + - - +
337C ILE* 4.0 31.2 - - + -
341C PHE* 3.8 30.1 - - + -
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Residues in contact with CYS 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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302C ILE* 5.0 4.7 - - - -
327C PHE* 3.0 51.3 + - - +
328C GLN* 3.8 10.1 - - - +
330C LEU* 1.3 76.7 - - - +
332C SER* 1.3 60.8 + - - +
334C SER 3.2 19.1 - - - +
335C PRO* 3.3 9.5 - - - +
338C ALA* 3.6 25.1 - - + +
341C PHE* 3.9 18.6 - - - -
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Residues in contact with SER 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 GLN 3.0 18.6 + - - -
329C MET* 3.8 4.9 - - - -
331C CYS* 1.3 76.2 - - - +
333C SER* 1.3 63.6 + - - +
334C SER 3.4 0.2 + - - -
335C PRO* 3.6 14.2 - - - +
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Residues in contact with SER 333 (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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239C LEU* 5.3 0.3 - - - +
243C VAL* 3.5 43.0 - - - +
329C MET* 2.9 30.4 + - - +
330C LEU* 3.7 3.8 - - - -
332C SER* 1.3 77.0 - - - +
334C SER* 1.3 59.2 + - - +
335C PRO* 3.7 5.0 - - - +
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Residues in contact with SER 334 (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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238C LYS* 4.7 6.5 + - - +
239C LEU* 3.6 25.8 - - - +
330C LEU 2.8 13.4 + - - +
331C CYS 3.2 6.0 - - - +
333C SER* 1.3 79.9 - - - +
335C PRO* 1.3 59.4 - - - +
336C GLU* 3.1 7.8 + - - +
337C ILE* 3.2 30.7 + - - +
338C ALA 3.0 21.7 + - - -
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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