Contacts of the helix formed by residues 326 - 344 (chain D) in PDB entry 7CAL
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 PRO 326 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C TYR* 3.7 42.8 - - + +
324D GLN 3.8 0.2 - - - -
325D LEU* 1.3 90.3 - - + +
327D HIS* 1.3 65.8 + - - +
328D ASP* 3.1 13.4 + - + +
329D ILE* 3.4 21.5 + - + +
330D GLN* 3.3 19.3 + - - +
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Residues in contact with HIS 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D LEU 3.9 0.2 + - - -
326D PRO* 1.3 74.6 - - - +
328D ASP* 1.3 66.3 + - - +
329D ILE 3.3 0.4 - - - -
330D GLN* 4.0 19.3 + - - -
331D ASP* 3.1 67.9 + - - +
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Residues in contact with ASP 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D PRO* 3.1 10.9 - - + +
327D HIS* 1.3 87.8 + - - +
329D ILE* 1.3 57.1 + - - +
331D ASP* 4.4 5.3 - - - +
332D GLN* 3.9 23.2 + - - +
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Residues in contact with ILE 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE* 4.5 11.4 - - + +
362C SER* 3.9 34.5 - - - +
363C ILE* 4.5 16.6 - - + -
366C TYR* 5.7 2.7 - - + -
325D LEU* 4.0 20.0 - - + -
326D PRO* 3.5 33.6 - - + +
328D ASP* 1.3 75.5 - - - +
330D GLN* 1.3 68.2 + - - +
331D ASP 3.3 1.6 - - - -
332D GLN* 3.3 35.9 + - + +
333D MET* 3.4 15.6 + - - +
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Residues in contact with GLN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D SER* 4.6 18.8 + - - +
320D ALA* 3.4 41.6 + - + +
321D SER* 5.4 1.8 - - - +
325D LEU* 4.6 7.4 - - + +
326D PRO 3.3 17.4 + - - +
327D HIS* 4.2 19.6 + - - +
328D ASP 3.7 0.2 - - - -
329D ILE* 1.3 80.4 - - - +
331D ASP* 1.3 64.9 + - - +
333D MET* 3.4 11.1 - - + +
334D LEU* 3.2 36.3 + - + +
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Residues in contact with ASP 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D HIS* 3.1 51.8 + - - +
328D ASP* 5.0 5.0 - - - +
329D ILE* 3.3 0.6 - - - +
330D GLN* 1.3 80.8 - - - +
332D GLN* 1.3 59.9 + - + +
333D MET 3.3 0.2 - - - -
334D LEU* 3.9 6.2 - - - +
335D SER* 2.6 37.4 + - - +
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Residues in contact with GLN 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ALA 5.3 1.2 - - - +
359C ILE* 3.4 31.6 - - + +
362C SER* 5.6 0.5 - - - -
328D ASP 3.9 15.6 + - - +
329D ILE* 3.3 28.5 + - + +
330D GLN 3.2 0.8 - - - -
331D ASP* 1.3 82.2 - - + +
333D MET* 1.3 59.7 + - - +
335D SER* 4.5 2.3 - - - -
336D HIS* 3.5 21.1 + - - +
399D PRO* 5.3 2.4 - - - +
401D LYS 3.7 24.0 + - - +
402D GLU* 4.7 6.3 - - + +
403D ASP* 3.6 34.2 + - - +
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Residues in contact with MET 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C THR* 5.2 3.1 - - + -
355C LEU* 3.9 32.5 - - + +
359C ILE* 3.7 19.0 - - + +
363C ILE* 4.0 12.6 - - + -
316D ALA* 4.0 30.3 - - + +
319D PHE* 4.2 15.0 - - + -
320D ALA* 4.1 18.6 - - - -
325D LEU* 4.5 9.6 - - - -
329D ILE 3.4 10.4 + - - +
330D GLN* 3.4 12.6 - - + +
332D GLN* 1.3 78.4 - - - +
334D LEU* 1.3 68.8 + - + +
336D HIS* 4.1 3.2 - - - +
337D ILE* 3.3 29.8 + - - +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ILE* 4.6 18.4 - - + -
313D VAL* 4.1 28.3 - - + +
316D ALA* 4.7 6.3 - - + +
317D SER* 3.8 25.4 - - - +
330D GLN* 3.2 35.6 + - + +
331D ASP* 4.5 5.4 - - - +
333D MET* 1.3 83.5 - - + +
335D SER* 1.3 62.8 + - - +
336D HIS 3.2 1.8 - - - -
337D ILE* 3.6 12.8 + - + +
338D CYS* 3.3 29.4 + - - -
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Residues in contact with SER 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ASP* 2.6 28.6 + - - +
332D GLN* 4.7 1.6 - - - -
334D LEU* 1.3 75.4 - - - +
336D HIS* 1.3 61.8 + - - +
338D CYS* 3.8 6.5 + - - +
339D LEU* 3.3 23.6 + - - +
399D PRO* 4.0 22.6 - - - +
400D PRO 6.0 0.4 - - - -
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Residues in contact with HIS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C ASN 4.2 11.5 + - - -
355C LEU* 4.9 9.0 - - + -
356C PRO* 3.9 36.8 - - + +
359C ILE* 5.4 4.7 - - + +
332D GLN 3.5 18.6 + - - +
333D MET* 4.3 5.6 - - - +
334D LEU 3.2 0.8 - - - -
335D SER* 1.3 77.5 - - - +
337D ILE* 1.3 64.5 + - + +
339D LEU* 3.4 1.8 + - - +
340D LYS* 2.9 49.3 + - + +
396D GLU 4.5 15.5 - - - -
397D TYR 5.1 1.7 + - - -
398D PHE* 5.2 10.3 - + - -
399D PRO* 4.3 21.1 - - + +
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C THR* 6.2 0.4 - - + -
355C LEU* 5.2 8.7 - - + -
309D PHE* 4.0 5.6 - - + -
312D SER* 3.7 30.5 - - - +
313D VAL* 3.9 17.0 - - + -
316D ALA* 3.7 28.3 - - + -
333D MET 3.3 20.2 - - - +
334D LEU* 3.6 11.6 + - + +
335D SER 3.5 0.4 - - - -
336D HIS* 1.3 81.3 - - + +
338D CYS* 1.3 62.5 + - - +
340D LYS* 3.5 7.7 + - + +
341D PHE* 3.1 22.9 + - - +
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Residues in contact with CYS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LYS 5.3 2.0 - - - -
189C ILE* 3.7 40.8 - - - -
309D PHE* 4.2 15.7 - - + -
313D VAL* 4.9 2.7 - - - -
334D LEU 3.3 18.3 + - - +
335D SER* 4.1 7.2 - - - +
336D HIS 3.3 0.4 - - - -
337D ILE* 1.3 78.1 - - - +
339D LEU* 1.3 60.3 + - - +
341D PHE* 3.6 3.6 + - - +
342D LYS* 3.3 30.9 + - + +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C TYR* 5.4 5.6 - - + -
335D SER 3.3 15.1 + - - +
336D HIS* 4.1 2.7 - - - +
337D ILE 3.3 0.4 - - - -
338D CYS* 1.3 77.7 - - - +
340D LYS* 1.3 63.8 + - - +
341D PHE 3.2 0.4 - - - -
342D LYS* 3.8 24.9 - - - +
343D THR* 2.8 47.7 + - + -
397D TYR* 3.3 29.6 - - + +
398D PHE 3.9 3.1 - - - +
399D PRO* 3.6 31.2 - - + -
400D PRO* 5.4 1.3 - - + -
461D THR* 4.8 11.7 - - + -
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Residues in contact with LYS 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C ASN* 3.5 41.7 + - + +
336D HIS* 2.9 40.5 + - + +
337D ILE* 3.9 7.2 - - + +
339D LEU* 1.3 77.8 - - - +
341D PHE* 1.3 58.8 + - - +
343D THR* 4.1 3.8 - - - -
344D GLU* 3.0 39.2 + - + +
345D GLY 3.3 6.8 - - - +
346D LEU 6.0 1.6 - - - -
396D GLU 6.1 1.8 - - - +
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Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LYS* 4.3 23.3 - - + -
305D ARG* 3.5 62.5 + - - -
306D THR* 4.6 6.1 - - - -
309D PHE* 3.8 44.2 - + + -
337D ILE 3.1 17.5 + - - +
338D CYS 3.6 5.4 + - - +
339D LEU 3.2 0.2 - - - -
340D LYS* 1.3 76.6 - - - +
342D LYS* 1.3 70.9 + - + +
343D THR 3.5 0.2 + - - -
345D GLY* 3.5 25.9 + - - +
346D LEU* 4.1 12.8 - - + -
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Residues in contact with LYS 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 4.8 6.1 + - - -
115C LEU* 5.0 19.4 - - - +
120C TYR* 3.7 32.2 + - + +
187C LYS* 6.5 1.1 - - - -
338D CYS* 3.3 19.6 + - + +
339D LEU* 3.5 23.9 + - + +
341D PHE* 1.3 86.0 - - + +
343D THR* 1.3 63.5 + - + +
345D GLY 4.8 0.4 + - - -
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Residues in contact with THR 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 2.9 29.0 + - - -
120C TYR* 3.6 36.6 + - + -
339D LEU* 2.8 39.2 + - + +
340D LYS* 4.1 2.6 + - - -
342D LYS* 1.3 82.1 - - - +
344D GLU* 1.3 69.2 + - - +
345D GLY 3.2 4.0 - - - -
348D GLN* 4.6 0.9 - - - +
396D GLU 5.4 0.2 + - - -
397D TYR* 3.8 33.1 - - + +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ARG* 3.7 6.0 + - - -
340D LYS* 3.0 31.9 + - + +
343D THR* 1.3 83.0 + - - +
345D GLY* 1.3 62.1 + - - +
346D LEU* 3.6 1.6 + - - -
348D GLN* 3.3 44.7 + - + +
395D ALA* 4.9 10.8 - - + +
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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