Contacts of the helix formed by residues 344 - 365 (chain A) in PDB entry 4CSC
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 ASP 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LEU* 3.2 18.6 + - + +
342A PRO 3.4 0.2 - - - -
343A GLY* 1.3 74.4 - - - +
345A PRO* 1.3 67.9 - - - +
346A MET* 2.8 31.2 + - - +
347A PHE* 2.8 17.4 + - + +
348A LYS* 2.7 35.0 + - - +
380A VAL* 4.2 0.3 - - - +
383A GLN* 3.3 25.9 + - - +
384A TYR* 3.9 28.9 - - + -
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Residues in contact with PRO 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY 3.1 9.8 - - - +
344A ASP* 1.3 98.0 - - - +
346A MET* 1.3 58.0 + - - +
348A LYS* 3.5 10.5 + - + +
349A LEU* 3.0 25.8 + - - +
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Residues in contact with MET 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.9 13.2 - - + +
285A LEU* 3.7 34.8 - - + +
286A ALA* 4.6 6.1 - - + +
289A GLN* 3.4 30.3 - - - +
344A ASP* 2.8 15.0 + - - +
345A PRO* 1.3 75.9 - - - +
347A PHE* 1.4 64.1 - - - +
349A LEU* 3.1 10.9 + - + +
350A VAL* 3.0 26.7 + - - +
380A VAL* 3.7 21.5 - - + -
383A GLN* 3.5 32.3 - - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG* 4.3 13.2 - - - -
337A ALA* 4.0 13.5 - - + -
338A LEU* 3.0 41.5 - - + -
341A LEU* 3.3 22.0 - - + +
342A PRO* 3.3 28.5 - - + -
344A ASP* 2.8 19.6 + - + +
346A MET* 1.4 74.6 - - - +
348A LYS* 1.3 58.8 + - + +
350A VAL* 3.2 3.5 + - + +
351A ALA* 2.8 35.1 + - + +
377A HIS* 3.9 34.8 - + - -
380A VAL* 3.5 14.6 - - + +
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A PRO 3.9 20.6 - - - +
343A GLY* 3.9 19.1 + - - +
344A ASP 2.7 21.7 + - - +
345A PRO* 3.6 9.0 - - + +
346A MET 3.2 0.2 - - - -
347A PHE* 1.3 76.6 - - + +
349A LEU* 1.3 56.0 + - - +
351A ALA* 3.2 8.1 + - - +
352A GLN* 2.9 28.7 + - - +
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Residues in contact with LEU 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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285A LEU* 3.8 25.6 - - + +
288A LEU* 4.5 8.7 - - + -
289A GLN* 3.4 34.3 - - - +
301A LEU* 4.1 24.5 - - + -
345A PRO 3.0 14.1 + - - +
346A MET* 3.1 16.6 + - + +
348A LYS* 1.3 76.3 - - - +
350A VAL* 1.3 56.8 + - - +
352A GLN* 2.9 18.2 + - - +
353A LEU* 2.8 37.8 + - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 5.8 0.2 - - + -
285A LEU* 3.7 19.5 - - + -
318A TYR* 5.0 0.5 + - - -
330A TYR* 3.7 13.3 + - + +
346A MET 3.0 6.8 + - - +
347A PHE* 3.4 8.5 - - - +
349A LEU* 1.3 69.9 - - - +
351A ALA* 1.3 68.4 + - - +
353A LEU* 3.5 10.3 + - + +
354A TYR 3.3 14.0 + - - -
376A ALA 4.1 15.0 - - - +
377A HIS* 3.7 39.3 - - + +
380A VAL* 3.2 32.1 - - + -
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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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330A TYR* 5.1 0.4 - - - -
334A ARG* 3.9 26.1 + - - +
347A PHE* 2.8 25.3 + - + +
348A LYS* 3.5 11.7 - - - +
349A LEU 3.2 0.2 - - - -
350A VAL* 1.3 78.9 - - - +
352A GLN* 1.3 63.8 + - - +
354A TYR* 3.1 17.9 + - - +
355A LYS* 3.5 12.6 + - - +
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Residues in contact with GLN 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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295A ALA* 6.2 0.4 - - - +
296A GLY 3.7 22.5 + - - +
298A ASP* 2.6 28.8 + - - +
301A LEU* 2.8 28.0 - - + +
348A LYS 2.9 12.8 + - - +
349A LEU* 2.9 23.0 + - - +
351A ALA* 1.3 78.6 - - - +
353A LEU* 1.3 58.2 + - - +
355A LYS* 3.0 25.6 + - + +
356A ILE* 3.1 19.7 - - + +
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Residues in contact with LEU 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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284A TRP* 4.1 11.2 - - + -
285A LEU* 3.4 33.0 - - + -
288A LEU* 4.4 9.0 - - + -
301A LEU* 3.9 29.2 - - + -
305A ILE* 4.2 10.5 - - + -
318A TYR* 3.8 8.7 - - + +
349A LEU* 2.8 26.6 + - + +
350A VAL* 3.7 10.3 - - + +
351A ALA 3.3 0.2 - - - -
352A GLN* 1.3 71.7 - - - +
354A TYR* 1.3 59.4 + - - +
355A LYS 2.9 2.7 - - - -
356A ILE* 2.8 7.5 + - + +
357A VAL* 2.6 55.7 + - + +
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Residues in contact with TYR 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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318A TYR* 3.4 8.2 + - - -
326A THR* 3.0 37.6 + - + +
330A TYR* 3.7 30.1 - + - +
334A ARG* 4.5 22.2 - - - -
350A VAL 3.3 2.4 + - - +
351A ALA* 3.1 14.0 + - - +
353A LEU* 1.3 78.5 - - - +
355A LYS* 1.3 66.3 + - + +
358A PRO* 3.3 16.5 - - + +
371A TRP* 3.9 17.2 - + - -
372A PRO* 3.8 24.2 - - + -
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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
----------------------------------------------------------
298A ASP* 5.9 2.2 - - - +
334A ARG* 5.8 5.5 - - - +
351A ALA* 3.8 13.7 - - - +
352A GLN* 3.0 15.0 + - + +
353A LEU 2.9 0.8 - - - -
354A TYR* 1.3 84.9 - - + +
356A ILE* 1.3 56.5 + - + +
358A PRO* 4.8 0.2 - - - -
359A ASN* 2.5 29.5 - - - +
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Residues in contact with ILE 356 (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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298A ASP* 3.5 33.7 - - + +
301A LEU* 3.1 33.0 - - + -
302A ARG* 4.3 18.4 - - + +
305A ILE* 3.9 20.9 - - + -
352A GLN* 3.1 21.9 + - + +
353A LEU* 2.8 8.9 + - - +
355A LYS* 1.3 83.7 - - + +
357A VAL* 1.3 66.5 - - - +
358A PRO 3.4 1.3 - - - -
359A ASN* 3.0 10.9 + - - +
360A VAL* 3.0 31.1 + - + +
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A TRP* 4.7 1.8 - - + -
305A ILE* 3.3 32.5 - - + -
315A VAL* 4.1 16.6 - - + -
318A TYR* 3.5 38.4 - - + -
353A LEU* 2.6 36.2 + - + +
356A ILE* 1.3 70.0 - - - +
358A PRO* 1.3 56.9 - - + +
360A VAL* 2.9 5.2 + - - +
361A LEU* 2.6 47.9 + - + +
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Residues in contact with PRO 358 (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 TYR* 3.6 20.2 - - + -
353A LEU 3.6 1.1 - - - +
354A TYR* 3.3 26.7 - - + +
355A LYS 5.4 0.2 - - - +
356A ILE 3.5 1.6 - - - -
357A VAL* 1.3 94.8 - - + +
359A ASN* 1.3 51.9 + - - +
361A LEU* 2.9 5.2 + - + +
362A LEU* 2.6 39.4 + - + +
370A PRO* 3.3 28.4 - - + +
371A TRP* 3.8 35.2 - - + -
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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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302A ARG* 5.7 5.8 - - - +
355A LYS 2.5 27.6 - - - +
356A ILE* 3.0 7.8 + - - +
358A PRO* 1.3 79.1 - - - +
360A VAL* 1.3 59.3 + - + +
362A LEU* 3.1 17.8 + - - +
363A GLU* 2.8 28.7 + - - +
371A TRP* 6.4 0.2 - - - -
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Residues in contact with VAL 360 (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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302A ARG* 3.9 37.5 - - + +
305A ILE* 3.8 27.8 - - + -
306A TRP* 3.6 28.7 - - + +
309A LEU* 3.8 10.8 - - + -
356A ILE* 3.0 21.4 + - + +
357A VAL 2.9 7.6 + - - +
359A ASN* 1.3 75.7 - - + +
361A LEU* 1.3 58.5 + - - +
363A GLU* 3.0 9.1 + - - +
364A GLN* 2.8 28.1 + - - +
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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
----------------------------------------------------------
305A ILE* 5.9 0.7 - - + -
309A LEU* 4.1 28.9 - - + -
315A VAL* 4.6 5.8 - - + -
318A TYR* 3.7 26.7 - - + -
357A VAL* 2.6 26.6 + - + +
358A PRO 3.3 8.7 - - - +
360A VAL* 1.3 74.3 - - + +
362A LEU* 1.3 59.3 + - - +
364A GLN* 3.5 11.4 + - - +
365A GLY* 3.3 17.3 + - - -
366A ALA 4.3 3.6 + - - -
367A ALA* 4.8 19.6 + - + +
369A ASN 4.9 0.7 - - - +
370A PRO* 3.5 35.9 - - + +
700A ACO 4.1 19.3 - - + +
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Residues in contact with LEU 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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358A PRO* 2.6 28.1 + - + +
359A ASN* 3.1 18.8 + - - +
361A LEU* 1.3 69.4 - - - +
363A GLU* 1.3 67.4 + - - +
365A GLY* 3.1 14.2 + - - -
370A PRO* 4.1 23.6 - - + -
371A TRP* 5.2 10.3 - - + -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ARG* 3.2 39.6 + - - -
306A TRP* 3.0 33.9 + - + -
359A ASN 2.8 11.4 + - - +
360A VAL* 3.0 11.7 + - - +
362A LEU* 1.3 79.1 - - - +
364A GLN* 1.3 64.6 + - - +
365A GLY* 3.1 1.6 + - - -
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Residues in contact with GLN 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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306A TRP* 3.7 24.4 - - + -
309A LEU* 3.4 50.1 - - + +
310A ASN* 5.7 0.3 + - - -
360A VAL 2.8 15.1 + - - +
361A LEU* 4.0 14.0 + - - +
362A LEU 3.3 0.4 - - - -
363A GLU* 1.3 75.2 - - - +
365A GLY* 1.3 60.8 + - - +
366A ALA* 4.4 20.9 - - + +
367A ALA 5.1 1.6 - - - +
700A ACO 4.4 8.7 + - - -
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Residues in contact with GLY 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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361A LEU 3.3 5.8 + - - -
362A LEU* 3.1 17.6 + - - -
363A GLU 4.1 0.7 - - - -
364A GLN* 1.3 76.8 - - - +
366A ALA* 1.3 59.2 + - - +
367A ALA 5.0 2.5 - - - -
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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
------------------------------------------------------------
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