Contacts of the helix formed by residues 350 - 368 (chain A) in PDB entry 3H1J
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 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER 3.6 13.2 - - - +
349A THR* 1.3 74.4 - - - +
351A GLU* 1.3 65.3 + - - +
352A SER* 3.5 10.8 + - - -
353A GLU* 2.7 54.1 + - - +
354A VAL* 3.2 13.9 + - - +
404A ALA* 3.9 2.9 - - - -
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 1.3 72.6 - - - +
352A SER* 1.3 64.2 + - - +
354A VAL* 2.9 31.9 - - - +
355A LYS* 2.9 9.1 + - - +
403A ASP* 3.8 18.9 - - - +
404A ALA* 3.1 36.9 + - + +
405A ARG* 4.2 1.0 + - - +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 3.1 9.3 - - - -
351A GLU* 1.3 78.1 - - - +
353A GLU* 1.3 63.1 + - - +
355A LYS* 3.4 10.1 + - - +
356A ARG* 3.2 22.5 + - - +
110S LYS* 3.2 32.2 + - - -
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Residues in contact with GLU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.8 28.3 - - + +
293A ARG* 4.2 19.8 - - - -
344A ARG* 5.4 5.3 - - - +
345A LEU* 6.0 0.2 - - - +
348A SER 4.0 1.3 - - - +
349A THR* 3.0 18.0 - - + +
350A THR* 2.7 53.2 + - + +
352A SER* 1.3 76.8 - - - +
354A VAL* 1.3 52.9 + - - +
356A ARG* 3.1 22.4 + - - +
357A ALA* 2.8 35.7 + - - +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 4.5 5.8 - - + -
276A ILE* 4.6 2.0 - - + -
349A THR* 3.6 19.1 - - + -
350A THR 3.7 1.8 - - - +
351A GLU* 2.9 37.5 - - - +
353A GLU* 1.3 74.4 - - - +
355A LYS* 1.3 55.2 + - + +
357A ALA* 3.8 8.7 - - - -
358A LYS* 2.7 50.9 + - + +
402A VAL 4.8 0.4 - - - +
403A ASP* 4.0 9.0 - - - -
404A ALA* 3.5 29.8 - - - +
407A VAL* 3.9 14.1 - - + -
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Residues in contact with LYS 355 (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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351A GLU 2.9 13.6 + - - +
352A SER* 3.5 13.9 - - - +
353A GLU 3.1 0.2 - - - -
354A VAL* 1.3 80.4 - - + +
356A ARG* 1.3 62.6 + - - +
358A LYS* 3.4 8.4 + - - +
359A ASN* 3.2 37.1 + - - +
91B ALA 5.3 2.9 - - - +
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Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA 4.5 4.0 + - - -
276A ILE* 3.1 44.2 + - - +
291A SER* 3.5 45.7 + - - -
292A SER* 4.3 1.0 - - - +
352A SER 3.2 9.1 + - - +
353A GLU* 3.1 28.5 + - - +
355A LYS* 1.3 79.1 - - - +
357A ALA* 1.3 59.3 + - - +
359A ASN* 3.1 4.0 + - - +
360A HIS* 2.9 31.2 + - + +
90B GLU* 3.1 31.1 - - - +
91B ALA* 4.0 17.9 - - - +
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Residues in contact with ALA 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.2 29.8 - - + +
275A ALA* 3.5 18.7 - - + +
276A ILE* 3.6 15.3 - - + +
353A GLU 2.8 20.9 + - - +
354A VAL* 3.5 8.1 - - - +
356A ARG* 1.3 74.9 - - - +
358A LYS* 1.3 56.4 + - - +
360A HIS* 3.3 1.9 + - - +
361A LEU* 2.8 31.3 + - - +
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A VAL* 3.9 15.9 - - + -
354A VAL* 2.7 39.9 + - + +
355A LYS* 3.8 7.9 - - - +
357A ALA* 1.3 71.0 - - - +
359A ASN* 1.3 63.2 + - - +
361A LEU* 3.2 6.1 + - - +
362A ARG* 2.9 43.4 + - - +
399A ILE* 3.2 38.0 - - + +
400A SER* 2.8 25.4 + - - +
402A VAL 2.8 27.8 + - - +
403A ASP* 5.5 0.4 - - - +
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Residues in contact with ASN 359 (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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355A LYS* 3.2 27.6 + - - +
356A ARG 3.1 7.2 + - - +
358A LYS* 1.3 78.1 - - - +
360A HIS* 1.3 65.0 + - - +
361A LEU 3.2 0.2 + - - -
362A ARG* 2.8 26.5 + - - +
363A SER* 3.1 24.3 + - - -
91B ALA 3.2 20.6 + - - +
92B VAL* 3.4 27.7 - - - +
93B GLY* 4.0 2.2 - - - -
112B LEU* 4.3 4.7 - - + +
115B HIS* 4.1 18.5 + - - -
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Residues in contact with HIS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA* 4.1 27.6 - - + +
278A GLY* 5.7 5.4 - - - -
279A ARG* 6.4 0.4 - - - +
356A ARG* 2.9 18.1 + - + +
357A ALA* 3.7 6.1 - - - +
359A ASN* 1.3 76.9 - - - +
361A LEU* 1.3 64.9 + - - +
363A SER* 3.2 6.5 + - - -
364A ALA* 3.1 26.9 + - + +
90B GLU 5.3 2.9 - - - +
93B GLY* 3.7 21.6 + - - -
94B GLY 5.8 0.8 + - - -
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Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.3 2.2 - - + +
271A HIS* 3.8 23.3 - - + +
272A VAL* 3.6 40.8 - - + +
275A ALA* 4.7 5.2 - - + -
357A ALA 2.8 17.0 + - - +
358A LYS* 3.4 6.1 - - - +
360A HIS* 1.3 77.3 - - - +
362A ARG* 1.3 54.9 + - - +
364A ALA* 2.9 12.7 + - + +
365A MET* 2.7 37.1 + - + +
399A ILE* 3.9 23.8 - - + -
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Residues in contact with ARG 362 (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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4A TYR* 3.2 29.9 - - - +
358A LYS* 2.9 34.1 + - - +
359A ASN* 2.8 44.0 + - - +
361A LEU* 1.3 74.6 - - - +
363A SER* 1.3 56.9 + - - +
365A MET* 3.1 20.7 + - + +
366A VAL* 2.9 32.2 + - - +
396A ASP* 3.2 17.2 + - - +
399A ILE* 4.2 14.9 - - + +
400A SER* 3.1 31.1 + - - +
112B LEU* 3.7 19.2 - - + +
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Residues in contact with SER 363 (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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359A ASN 3.1 10.9 + - - -
360A HIS* 3.3 12.3 - - - -
361A LEU 3.1 0.2 - - - -
362A ARG* 1.3 77.6 - - - +
364A ALA* 1.3 60.0 + - - +
366A VAL* 3.5 5.4 + - - +
367A ALA* 3.1 21.3 + - - +
92B VAL 4.3 0.2 + - - -
93B GLY* 2.8 29.3 + - - -
111B CYS* 5.0 1.7 - - - -
112B LEU* 3.7 27.1 + - - +
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Residues in contact with ALA 364 (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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360A HIS* 3.1 19.7 + - + +
361A LEU* 2.9 17.6 + - + +
363A SER* 1.3 73.8 - - - +
365A MET* 1.3 67.2 + - - +
367A ALA* 3.0 16.2 + - - +
368A GLN* 3.0 24.1 + - + +
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Residues in contact with MET 365 (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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4A TYR* 3.8 18.2 - - - +
8A LEU* 5.5 0.4 - - + -
361A LEU* 2.7 15.8 + - + +
362A ARG* 3.1 35.4 - - + +
364A ALA* 1.3 76.9 - - - +
366A VAL* 1.3 62.9 + - + +
368A GLN* 3.2 24.1 - - - +
369A LEU* 4.1 2.8 + - - +
392A LEU* 3.6 42.7 - - + +
395A TRP* 3.3 37.7 - - + -
396A ASP* 4.3 4.3 - - + -
399A ILE* 3.9 13.2 - - + -
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 4.9 2.5 - - + -
8A LEU* 5.6 0.2 - - + -
362A ARG 2.9 16.6 + - - +
363A SER* 3.6 9.9 - - - +
365A MET* 1.3 80.1 - - + +
367A ALA* 1.3 58.4 + - - +
368A GLN 2.9 4.9 - - - -
369A LEU* 2.9 29.3 + - - +
370A ASP* 4.7 0.9 - - - +
392A LEU* 4.2 15.3 - - + -
42B SER* 5.1 2.5 - - - +
43B PRO* 4.1 28.0 - - + -
44B ALA* 3.7 26.2 - - + -
112B LEU* 4.0 16.4 - - + -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER 3.1 12.8 + - - +
364A ALA* 3.0 13.4 + - - +
366A VAL* 1.3 77.5 - - - +
368A GLN* 1.3 61.8 + - - +
369A LEU 3.0 2.6 + - - -
370A ASP* 3.5 23.3 + - + +
374A PRO* 5.0 2.4 - - - +
110B GLU* 6.0 1.6 - - - +
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA* 3.0 24.9 + - - +
365A MET* 3.2 18.4 - - - +
366A VAL 2.9 0.8 - - - -
367A ALA* 1.3 80.2 + - - +
369A LEU* 1.3 71.9 + - + +
370A ASP 3.6 0.7 - - - -
374A PRO* 3.3 18.7 - - - +
378A THR* 3.7 9.6 + - + +
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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
------------------------------------------------------------
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