Contacts of the helix formed by residues 335 - 345 (chain A) in PDB entry 4HS2
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A VAL* 3.5 44.6 + - + +
300A GLU* 4.1 12.4 + - + -
303A ALA* 5.1 1.7 + - - +
331A ASP 3.7 3.8 - - - +
332A VAL* 2.7 24.9 + - - +
333A LEU 3.3 0.2 - - - -
334A GLU* 1.3 80.0 - - - +
336A SER* 1.3 64.1 + - - +
337A GLY* 3.8 4.5 + - - -
338A TRP* 3.2 15.1 + - - +
339A LYS* 3.1 26.5 + - - +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 5.7 0.3 + - - -
334A GLU 4.1 0.8 + - - -
335A THR* 1.3 73.7 - - - +
337A GLY* 1.3 59.1 + - - +
339A LYS* 3.8 9.7 - - - +
340A SER* 2.9 38.3 + - - -
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Residues in contact with GLY 337 (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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300A GLU 5.1 5.1 + - - -
303A ALA* 3.5 12.4 - - - +
304A GLU* 4.3 29.1 + - - +
307A ILE* 5.1 1.7 - - - +
335A THR* 3.2 5.7 + - - -
336A SER* 1.3 80.6 + - - +
338A TRP* 1.3 60.8 + - - +
340A SER* 3.9 5.0 - - - -
341A MET* 3.0 24.3 + - - +
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Residues in contact with TRP 338 (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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303A ALA* 3.5 12.1 - - + +
325A ILE* 3.9 21.8 - - + -
332A VAL* 3.2 40.4 - - + +
333A LEU* 3.6 46.0 - - + +
335A THR* 3.2 8.5 + - - +
337A GLY* 1.3 73.7 - - - +
339A LYS* 1.3 72.0 + - + +
341A MET* 3.0 30.2 + - + +
342A VAL* 2.9 41.6 + - + +
349A VAL* 3.9 32.5 - - + -
352A ALA* 4.9 10.5 - - + -
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Residues in contact with LYS 339 (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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333A LEU 3.6 23.3 - - - +
334A GLU* 4.0 27.7 + - - +
335A THR 3.1 15.5 + - - +
336A SER* 3.3 7.4 + - - +
338A TRP* 1.3 82.4 - - + +
340A SER* 1.3 62.2 + - - +
342A VAL* 3.5 17.4 + - - +
343A VAL* 3.8 11.3 + - - +
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Residues in contact with SER 340 (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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336A SER* 2.9 21.2 + - - -
337A GLY* 3.9 5.2 - - - -
339A LYS* 1.3 74.9 - - - +
341A MET* 1.3 60.0 + - - +
343A VAL* 3.3 7.1 + - - +
344A SER* 2.9 31.9 + - - -
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Residues in contact with MET 341 (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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303A ALA* 3.7 25.6 - - + +
306A LEU* 4.0 17.0 - - + -
307A ILE* 3.8 25.5 - - + +
337A GLY 3.0 18.2 + - - +
338A TRP* 3.0 41.1 + - + +
340A SER* 1.3 74.3 - - - +
342A VAL* 1.3 60.7 + - - +
344A SER* 3.5 8.3 - - - -
345A HIS* 2.8 42.1 + - + +
348A LEU* 4.0 11.0 - - - -
349A VAL* 3.8 25.6 - - + +
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Residues in contact with VAL 342 (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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338A TRP* 2.9 48.3 + - + +
339A LYS* 3.6 11.4 - - - +
340A SER 3.3 0.4 - - - -
341A MET* 1.3 77.4 - - - +
343A VAL* 1.3 64.5 + - + +
346A PRO* 3.6 22.3 - - - +
349A VAL* 3.8 19.7 - - + -
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Residues in contact with VAL 343 (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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339A LYS 3.8 11.6 + - - +
340A SER* 3.3 7.7 + - - +
341A MET 3.2 0.4 - - - -
342A VAL* 1.3 84.4 - - + +
344A SER* 1.3 65.3 + - - +
346A PRO* 3.6 9.9 - - - +
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Residues in contact with SER 344 (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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307A ILE* 4.2 3.5 - - - +
340A SER* 2.9 20.3 + - - -
341A MET* 3.5 7.1 - - - -
343A VAL* 1.3 80.2 - - - +
345A HIS* 1.3 94.4 + - - +
346A PRO* 3.5 4.6 - - - +
347A HIS* 5.4 0.3 - - - -
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Residues in contact with HIS 345 (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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307A ILE* 3.7 35.9 - - + +
310A ASP* 4.9 4.3 - - - -
341A MET* 2.8 23.4 + - + +
344A SER* 1.3 106.1 + - - +
346A PRO* 1.3 67.2 - - - +
347A HIS* 3.1 27.1 - + + -
348A LEU* 2.9 38.7 + - + +
349A VAL 3.6 2.9 + - - -
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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