Contacts of the helix formed by residues 338 - 351 (chain A) in PDB entry 5F85
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 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A SER* 4.6 0.2 - - - -
336A TYR 3.6 2.8 + - - -
337A PRO* 1.3 76.1 - - - +
339A GLN* 1.3 63.5 + - - +
340A GLN* 3.7 10.1 + - - +
341A GLU* 2.9 28.5 + - - +
342A TYR* 3.1 24.0 + - - -
507A SO4 3.5 24.2 - - - -
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Residues in contact with GLN 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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239A SER* 3.7 18.2 - - - +
242A LEU* 3.7 22.8 - - - +
243A LEU* 3.4 28.1 - - + +
246A ARG* 2.8 50.1 + - - +
338A SER* 1.3 73.3 - - - +
340A GLN* 1.3 57.5 + - + +
342A TYR* 3.3 10.0 + - - +
343A GLU* 3.0 34.9 + - - +
507A SO4 2.8 30.6 + - - +
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Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 6.3 0.7 - - - +
338A SER* 3.2 7.7 - - - +
339A GLN* 1.3 77.0 - - + +
341A GLU* 1.3 62.0 + - - +
343A GLU* 3.4 16.1 + - - +
344A HIS* 2.7 46.7 + - + +
507A SO4 5.2 5.5 + - - -
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Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.8 29.2 - - - -
49A LYS* 5.2 5.5 + - - -
333A LEU* 4.0 26.8 - - + +
337A PRO* 4.7 10.8 - - + -
338A SER* 2.9 29.4 + - - +
340A GLN* 1.3 75.4 - - - +
342A TYR* 1.3 59.6 + - - +
344A HIS* 3.3 4.3 + - - +
345A ILE* 2.9 32.6 + - - +
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Residues in contact with TYR 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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236A GLU 4.5 0.2 + - - -
239A SER* 3.3 23.9 + - - -
240A LEU* 3.4 31.8 + - + +
243A LEU* 3.5 15.5 - - + -
288A PHE* 3.5 34.8 - + - -
290A PHE* 3.2 31.4 - + - -
333A LEU* 3.7 19.1 - - + -
337A PRO* 3.5 22.6 - - + +
338A SER 3.1 19.0 + - - -
339A GLN* 3.5 11.7 - - - +
341A GLU* 1.3 75.3 - - - +
343A GLU* 1.3 63.9 + - - +
345A ILE* 3.3 6.0 + - + +
346A LEU* 3.0 34.6 + - + +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.7 9.6 - - + +
246A ARG* 3.2 31.7 + - - -
247A ASN* 4.8 5.6 + - - +
250A LEU* 3.8 26.9 - - + +
339A GLN 3.0 19.2 + - - +
340A GLN* 3.7 20.7 - - - +
342A TYR* 1.3 75.4 - - - +
344A HIS* 1.3 65.2 + - + +
346A LEU* 4.2 0.3 - - - +
347A SER* 3.0 27.4 + - - -
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Residues in contact with HIS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.6 26.0 + - - -
43A GLU* 5.5 4.0 - - + -
46A PHE* 3.2 53.0 - + + -
340A GLN* 2.7 46.6 + - + +
341A GLU* 3.3 3.8 + - - +
343A GLU* 1.3 80.3 - - + +
345A ILE* 1.3 59.0 + - - +
347A SER* 3.8 4.8 - - - -
348A PHE* 3.1 21.5 + - - +
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Residues in contact with ILE 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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46A PHE* 3.9 8.1 - - + -
50A ILE* 3.6 28.7 - - + -
288A PHE* 5.3 0.2 - - + -
310A PHE* 3.8 28.9 - - + -
327A TRP* 4.2 6.5 - - + -
331A VAL* 4.0 13.5 - - + -
332A PRO 5.4 0.2 - - - +
333A LEU* 4.2 23.3 - - + -
341A GLU* 2.9 18.8 + - - +
342A TYR* 3.3 17.9 - - + +
344A HIS* 1.3 75.3 - - - +
346A LEU* 1.3 70.8 + - + +
348A PHE* 3.4 2.1 + - - +
349A PHE* 3.1 39.7 + - + -
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Residues in contact with LEU 346 (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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226A GLY* 4.4 2.7 - - - +
250A LEU* 3.8 27.1 - - + +
251A VAL* 3.6 31.0 - - + -
286A TYR* 3.8 40.5 - - + -
288A PHE* 3.9 25.1 - - + -
310A PHE* 4.2 8.7 - - + -
342A TYR* 3.0 23.9 + - + +
343A GLU 4.2 1.3 - - - +
345A ILE* 1.3 77.4 - - + +
347A SER* 1.3 60.1 + - - +
349A PHE* 3.2 3.3 + - - +
350A LYS* 2.9 38.7 + - + +
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Residues in contact with SER 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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43A GLU* 5.0 3.8 + - - -
250A LEU* 5.3 3.0 - - - +
343A GLU 3.0 21.3 + - - -
344A HIS* 3.8 5.6 - - - -
346A LEU* 1.3 76.3 - - - +
348A PHE* 1.3 61.5 + - - +
350A LYS* 3.6 10.9 + - - +
351A LYS* 3.3 48.4 + - - +
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 5.8 1.3 - - - -
46A PHE* 4.3 10.1 - + + -
47A SER* 3.6 44.4 - - - -
50A ILE* 3.8 23.3 - - + -
51A ARG* 3.8 23.3 - - + -
344A HIS 3.1 18.9 + - - +
345A ILE* 3.6 4.9 - - - +
346A LEU 3.2 0.4 - - - -
347A SER* 1.3 76.6 - - - +
349A PHE* 1.3 93.4 + + - +
351A LYS* 3.2 3.9 + - - -
352A ASN* 2.8 51.6 + - + +
355A LEU* 4.0 14.4 - - + -
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Residues in contact with PHE 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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50A ILE* 4.5 0.7 - - + -
54A ILE* 4.5 4.7 - - + -
286A TYR* 4.0 13.4 + - + -
308A LEU* 3.8 20.0 - - + -
310A PHE* 4.1 11.7 - + + -
327A TRP* 3.8 16.6 - + - -
331A VAL* 3.5 26.0 - - + -
345A ILE* 3.1 47.8 + - + +
346A LEU 3.2 2.0 + - - +
348A PHE* 1.3 100.9 - + - +
350A LYS* 1.3 60.1 + - - +
352A ASN 3.1 17.2 + - - +
353A ASP* 3.2 15.1 + - - -
355A LEU* 4.6 3.4 - - + -
356A ALA* 3.9 19.3 - - + +
359A ILE* 3.6 23.3 - - + -
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Residues in contact with LYS 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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224A SER* 4.2 26.9 + - - +
249A GLU 5.1 5.3 + - - -
250A LEU* 3.5 28.9 - - + +
286A TYR* 3.3 29.5 + - + +
346A LEU* 2.9 25.3 + - + +
347A SER* 3.7 8.7 - - - +
349A PHE* 1.3 76.9 - - - +
351A LYS* 1.3 59.9 + - + +
352A ASN 3.3 0.2 - - - -
353A ASP* 4.6 8.7 + - - +
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Residues in contact with LYS 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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43A GLU* 3.2 34.9 + - - +
347A SER* 3.3 31.1 + - - +
348A PHE* 3.2 2.1 + - - -
349A PHE 3.2 0.6 - - - -
350A LYS* 1.3 79.5 - - + +
352A ASN* 1.3 78.4 + - - +
353A ASP 3.8 1.3 - - - -
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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