Contacts of the helix formed by residues 343 - 354 (chain A) in PDB entry 1O7F
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A LEU* 1.3 76.7 - - - +
344A THR* 1.3 63.4 + - - +
345A THR* 2.8 21.7 + - - +
346A VAL* 3.1 22.2 + - - +
347A LYS* 2.8 26.7 + - - +
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Residues in contact with THR 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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330A TYR* 3.4 26.1 - - - +
334A LEU* 5.7 1.6 - - + -
343A SER* 1.3 74.8 + - - +
345A THR* 1.3 74.5 + - - +
347A LYS* 3.1 15.5 + - - +
348A ARG* 2.8 32.0 + - - +
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Residues in contact with THR 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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343A SER* 2.8 19.1 + - - +
344A THR* 1.3 90.7 + - - +
346A VAL* 1.3 65.2 + - - +
348A ARG* 3.3 10.4 - - - +
349A GLU* 3.2 29.7 + - - +
442A VAL* 4.6 12.0 - - - +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.1 26.0 - - + -
343A SER* 3.1 28.6 + - - +
345A THR* 1.3 83.3 + - - +
347A LYS* 1.3 65.6 + - - +
349A GLU* 3.2 5.9 + - - +
350A LEU* 3.0 22.2 + - + +
435A PHE* 4.6 12.6 - - + -
438A ILE* 4.3 16.1 - - + +
439A LEU* 4.6 11.2 - - + -
442A VAL* 4.3 23.1 - - + -
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Residues in contact with LYS 347 (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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330A TYR* 3.9 11.8 - - + -
333A LEU* 3.7 26.1 + - + +
334A LEU* 3.4 34.9 + - + +
339A LEU* 3.6 29.3 + - + +
340A SER* 5.2 5.1 - - - +
342A LEU* 3.3 34.8 + - + -
343A SER 2.8 14.1 + - - +
344A THR* 3.7 16.1 - - - +
346A VAL* 1.3 76.2 - - - +
348A ARG* 1.3 63.9 + - - +
350A LEU* 3.2 20.5 + - + +
351A ALA 3.3 8.3 + - - -
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Residues in contact with ARG 348 (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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326A LEU* 5.7 1.7 - - - +
327A GLU* 5.4 14.3 + - - +
330A TYR* 3.4 54.5 + - + +
331A ASP* 5.8 0.2 + - - -
344A THR* 2.8 14.0 + - - +
345A THR* 3.3 15.0 - - - +
347A LYS* 1.3 78.9 - - - +
349A GLU* 1.3 69.1 + - - +
351A ALA* 3.4 15.2 + - - +
352A GLY 4.3 1.4 + - - -
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Residues in contact with GLU 349 (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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345A THR* 3.2 15.6 - - - +
346A VAL 3.2 2.1 + - - +
348A ARG* 1.3 82.7 - - - +
350A LEU* 1.3 62.5 + - - +
352A GLY* 3.2 13.0 + - - -
353A VAL* 3.7 6.4 + - - +
438A ILE* 3.5 40.8 - - + +
441A ASP* 4.9 11.9 - - + +
442A VAL* 4.5 10.3 - - + -
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Residues in contact with LEU 350 (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* 4.4 6.3 - - + -
339A LEU* 4.2 19.7 - - + -
342A LEU* 4.0 27.6 - - + -
346A VAL* 3.0 13.2 + - + +
347A LYS* 3.2 20.2 + - + +
349A GLU* 1.3 76.5 - - - +
351A ALA* 1.3 54.0 + - - +
353A VAL* 3.7 17.0 - - + +
354A LEU* 2.7 45.7 + - + +
376A TRP* 5.6 0.4 - - + -
430A VAL* 4.0 31.9 - - + -
435A PHE* 4.8 10.1 - - + -
438A ILE* 4.0 12.3 - - + +
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Residues in contact with ALA 351 (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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321A ARG* 2.9 20.6 + - - -
326A LEU* 3.6 27.9 - - + +
329A ILE* 3.5 40.5 - - + +
330A TYR* 4.1 5.6 - - + +
333A LEU* 4.2 4.0 - - + +
347A LYS 3.3 8.1 + - - +
348A ARG 3.7 11.0 - - - +
349A GLU 3.2 0.8 - - - -
350A LEU* 1.3 78.9 - - - +
352A GLY* 1.3 57.0 + - - +
353A VAL 3.4 0.2 + - - -
354A LEU* 4.0 2.9 + - - +
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Residues in contact with GLY 352 (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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318A PRO* 3.1 34.2 - - - +
321A ARG* 3.5 4.3 - - - -
326A LEU* 3.6 22.2 - - - +
348A ARG 4.3 1.6 + - - -
349A GLU 3.2 8.5 + - - -
350A LEU 3.2 0.6 - - - -
351A ALA* 1.3 79.3 - - - +
353A VAL* 1.3 60.1 + - - +
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Residues in contact with VAL 353 (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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318A PRO* 4.2 12.0 - - + +
321A ARG* 4.1 0.2 - - - -
349A GLU 3.7 8.0 + - - +
350A LEU* 3.1 22.1 + - + +
352A GLY* 1.3 82.4 - - - +
354A LEU* 1.3 72.4 + - - +
355A ILE* 3.6 11.6 + - - +
429A ARG 4.8 0.7 - - - +
430A VAL* 5.4 5.6 - - + -
431A ASP 5.7 2.0 - - - +
434A ASP* 3.4 47.7 - - + +
437A ARG* 3.6 15.9 - - - +
438A ILE* 4.1 10.3 - - + -
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Residues in contact with LEU 354 (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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314A LEU* 4.2 16.3 - - + +
318A PRO* 4.4 0.7 - - - +
321A ARG* 3.1 25.0 + - - +
329A ILE* 4.5 8.5 - - + -
333A LEU* 3.3 38.8 - - + -
339A LEU* 5.9 2.2 - - + -
350A LEU* 2.7 33.0 + - + +
351A ALA 4.4 2.0 - - - +
352A GLY 3.8 0.4 - - - -
353A VAL* 1.3 79.7 - - - +
355A ILE* 1.3 61.5 + - - +
378A ILE* 5.9 0.9 - - + -
428A LEU* 3.8 33.0 - - + -
429A ARG 3.7 17.5 - - - +
430A VAL* 3.7 21.1 - - + -
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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