Contacts of the helix formed by residues 330 - 335 (chain H) in PDB entry 3SRF
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 LEU 330 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329H MET* 1.3 95.4 - - - +
331H GLU* 1.3 57.2 + - - +
332H SER 3.2 3.4 - - - -
333H MET* 2.9 44.4 + - + +
339H PRO* 3.9 12.6 - - + -
343H GLU* 3.7 22.4 - - + +
344H GLY 4.5 0.4 - - - +
347H VAL* 3.6 18.2 - - + -
360H LEU* 4.1 7.0 - - + -
363H GLU* 3.0 29.4 + - + +
373H ALA 3.7 23.1 - - - +
376H MET* 4.3 9.2 - - + -
377H GLN* 3.9 19.7 - - + +
380H ILE* 4.7 4.0 - - + -
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Residues in contact with GLU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340G THR* 4.5 15.7 - - + +
177H ASP* 5.5 2.6 - - - +
328H GLN* 3.4 50.4 + - + +
329H MET 3.8 0.8 - - - -
330H LEU* 1.3 75.0 - - - +
332H SER* 1.3 61.1 + - - +
334H ILE* 3.2 47.5 + - - +
335H LYS 4.6 0.2 + - - -
343H GLU* 3.5 9.9 + - + +
363H GLU* 4.2 4.7 - - - +
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Residues in contact with SER 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H GLU* 1.3 71.3 - - - +
333H MET* 1.3 56.2 + - - +
334H ILE 3.1 7.3 + - - -
335H LYS* 3.2 5.0 + - - +
336H LYS* 2.8 40.3 + - - +
338H ARG 3.7 3.4 + - - -
339H PRO* 3.4 6.1 - - - +
340H THR* 3.3 28.1 + - - +
343H GLU* 2.5 34.7 + - - -
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Residues in contact with MET 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330H LEU* 2.9 35.8 + - + +
332H SER* 1.3 74.1 + - - +
334H ILE* 1.3 62.0 + - - +
335H LYS 3.4 0.2 - - - -
336H LYS 3.0 15.4 - - - +
337H PRO* 3.2 28.7 - - + +
338H ARG* 3.8 3.4 - - - +
339H PRO* 3.6 40.2 - - + -
363H GLU* 4.7 4.2 - - + +
369H TYR* 3.5 23.9 + - - +
372H GLU* 3.3 34.5 - - + +
373H ALA* 3.7 18.6 - - + +
376H MET* 4.1 7.0 - - + -
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Residues in contact with ILE 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330H LEU 4.0 0.2 + - - -
331H GLU* 3.2 39.9 - - - +
332H SER 3.1 0.6 - - - -
333H MET* 1.3 78.8 - - - +
335H LYS* 1.3 70.7 + - + +
361H SER 5.4 0.2 - - - +
362H GLY* 3.8 20.4 - - - +
363H GLU* 3.7 26.5 - - + +
366H LYS* 5.1 9.0 - - + +
367H GLY* 3.7 20.0 - - - +
368H ASP* 2.9 32.2 + - - +
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Residues in contact with LYS 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331H GLU 4.6 0.2 + - - -
332H SER 3.2 5.0 + - - +
334H ILE* 1.3 89.0 + - + +
336H LYS* 1.3 71.9 + - + +
368H ASP* 3.4 24.6 + - - +
369H TYR* 3.5 16.4 + - - -
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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