Contacts of the helix formed by residues 400 - 418 (chain D) in PDB entry 3A13
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 GLY 400 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D THR 4.7 0.2 - - - -
397D HIS* 2.9 18.4 + - - +
398D PRO 3.4 2.0 + - - -
399D ASP* 1.3 77.9 - - - +
401D PRO* 1.3 76.6 - - - +
402D ALA 3.5 2.0 - - - -
403D ALA* 3.1 7.5 + - - +
404D GLY 3.1 16.8 + - - -
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Residues in contact with PRO 401 (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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176D LEU* 3.8 31.0 - - + -
179D ASP* 5.9 2.2 - - + -
180D LEU* 3.6 16.7 - - + +
394D THR* 3.9 12.6 - - - +
395D LEU* 4.5 21.8 - - + +
400D GLY* 1.3 84.9 - - - +
402D ALA* 1.3 65.1 + - - +
404D GLY* 2.9 13.0 + - - -
405D ALA 3.0 10.4 + - - -
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Residues in contact with ALA 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASP* 4.5 14.7 - - + +
180D LEU* 4.3 7.4 - - - +
183D ASN* 3.4 33.3 - - - +
400D GLY 3.5 0.8 + - - -
401D PRO* 1.3 78.7 - - - +
403D ALA* 1.3 59.6 + - - +
405D ALA 3.5 0.7 + - - -
406D ARG* 3.2 35.3 + - - +
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Residues in contact with ALA 403 (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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397D HIS* 4.0 10.5 - - + +
399D ASP* 3.6 29.4 + - + +
400D GLY 3.1 11.0 + - - +
401D PRO 3.1 0.4 - - - -
402D ALA* 1.3 74.9 - - - +
404D GLY* 1.3 56.1 + - - +
405D ALA 3.0 1.6 - - - -
406D ARG* 2.8 22.6 + - - +
407D ALA* 2.5 35.9 + - - +
430D GLU* 4.0 8.0 - - + +
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Residues in contact with GLY 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D PRO* 4.9 0.2 - - - +
393D GLY 4.6 1.4 - - - +
394D THR* 3.7 16.1 - - - -
397D HIS* 3.4 29.4 - - - -
400D GLY 3.1 4.8 + - - -
401D PRO 2.9 8.5 + - - -
403D ALA* 1.3 79.4 - - - +
405D ALA* 1.3 54.0 + - - +
407D ALA* 3.4 2.8 - - - +
408D VAL* 3.0 32.7 + - - +
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Residues in contact with ALA 405 (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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158D TYR* 3.5 25.7 - - + +
180D LEU* 3.7 34.1 - - + +
183D ASN* 3.7 18.3 - - + +
185D ALA* 5.1 0.4 - - + -
394D THR* 3.7 0.8 - - + +
401D PRO 3.0 4.6 + - - -
402D ALA 3.8 8.3 - - - +
403D ALA 3.0 0.2 - - - -
404D GLY* 1.3 73.7 - - - +
406D ARG* 1.3 64.9 + - - +
408D VAL* 3.3 2.6 + - - +
409D ARG* 3.2 23.4 + - - +
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Residues in contact with ARG 406 (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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183D ASN* 2.7 58.8 + - + +
402D ALA* 3.2 14.8 + - - +
403D ALA* 2.8 26.9 + - - +
405D ALA* 1.3 75.3 - - - +
407D ALA* 1.3 60.3 + - - +
409D ARG* 3.3 5.1 + - - +
410D GLN* 2.8 41.7 + - - +
430D GLU* 4.4 10.2 - - + +
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Residues in contact with ALA 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D PRO* 3.7 13.9 - - + +
397D HIS* 3.6 12.6 - - + -
403D ALA 2.5 20.5 + - - +
404D GLY 3.4 7.2 - - - +
406D ARG* 1.3 74.3 - - - +
408D VAL* 1.3 56.7 + - - +
410D GLN* 3.5 4.9 - - - +
411D ALA* 3.2 25.5 + - - +
430D GLU* 3.0 36.7 - - - +
431D LEU* 4.0 4.7 - - - +
434D ALA* 4.5 0.4 - - + -
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Residues in contact with VAL 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D TYR* 3.3 50.9 - - + +
372D PRO* 3.9 14.4 - - + -
375D ILE* 5.1 2.5 - - + -
390D LEU* 3.7 31.2 - - + -
393D GLY 4.2 7.0 - - - +
394D THR* 4.2 1.8 - - - +
404D GLY 3.0 19.6 + - - +
405D ALA 3.7 1.6 - - - +
406D ARG 3.0 0.8 - - - -
407D ALA* 1.3 76.3 - - - +
409D ARG* 1.3 59.6 - - - +
410D GLN 3.1 1.1 - - - -
411D ALA* 4.0 2.5 - - - +
412D ILE* 3.1 33.9 + - + +
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Residues in contact with ARG 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ARG* 2.4 64.1 - - - +
158D TYR* 4.3 11.0 - - + -
184D GLY* 3.3 37.6 + - - +
186D ASP* 4.2 1.6 + - - -
222D GLU* 3.4 27.9 + - - -
224D LYS* 5.5 0.8 - - - +
405D ALA 3.2 17.9 + - - +
406D ARG* 3.3 5.8 + - - +
408D VAL* 1.3 73.9 - - - +
410D GLN* 1.3 62.1 + - - +
412D ILE* 3.8 12.7 - - - +
413D ASP* 2.8 37.1 + - - +
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Residues in contact with GLN 410 (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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406D ARG* 2.8 25.4 + - + +
407D ALA 3.5 4.9 - - - +
408D VAL 3.1 0.2 - - - -
409D ARG* 1.3 75.5 - - - +
411D ALA* 1.3 55.4 + - - +
413D ASP* 2.5 41.1 + - - +
414D ALA* 3.2 5.4 + - - +
428D HIS* 3.1 36.5 + - + +
429D LYS 4.6 0.4 - - - +
430D GLU* 3.0 31.3 - - - +
431D LEU* 2.5 43.4 + - + +
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Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D PRO* 3.4 46.7 - - + +
375D ILE* 4.5 10.7 - - + +
407D ALA 3.2 5.5 + - - +
408D VAL 4.1 3.8 - - - +
410D GLN* 1.3 79.0 - - - +
412D ILE* 1.3 59.5 + - - +
414D ALA* 3.6 10.6 - - - +
415D ILE* 3.3 19.6 + - - +
421D LEU* 5.8 6.7 - - + +
431D LEU* 4.8 6.3 - - + +
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Residues in contact with ILE 412 (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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155D ARG* 5.0 11.7 - - - +
156D PRO* 4.5 20.4 - - + +
158D TYR* 4.1 22.9 - - + -
375D ILE* 3.7 17.7 - - + -
379D ILE* 5.0 4.5 - - + -
388D LEU* 4.1 21.5 - - + -
408D VAL* 3.1 26.5 + - + +
409D ARG* 3.9 13.9 - - - +
410D GLN 2.8 2.8 + - - -
411D ALA* 1.3 71.6 - - - +
413D ASP* 1.3 64.3 + - - +
415D ILE* 3.1 6.7 + - - +
416D MET* 2.8 42.3 + - + +
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Residues in contact with ASP 413 (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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409D ARG* 2.8 30.4 + - - +
410D GLN* 2.5 21.2 + - - +
412D ILE* 1.3 75.8 - - - +
414D ALA* 1.3 54.1 + - - +
416D MET* 3.3 5.8 + - - +
417D GLN* 2.9 36.6 + - + +
428D HIS* 6.0 3.4 - - + -
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Residues in contact with ALA 414 (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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410D GLN 3.2 4.2 + - - +
411D ALA* 3.6 15.9 - - - +
413D ASP* 1.3 78.7 - - - +
415D ILE* 1.3 55.9 + - - +
417D GLN* 4.6 1.1 - - - -
418D GLY 3.0 27.4 + - - -
419D ILE* 2.9 37.1 + - - +
421D LEU* 4.6 11.9 - - + +
424D TYR* 4.5 17.7 - - + +
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Residues in contact with ILE 415 (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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375D ILE* 5.4 1.1 - - + +
376D GLN* 5.4 9.4 - - + -
379D ILE* 3.8 33.8 - - + +
411D ALA 3.3 9.5 + - - +
412D ILE 3.1 8.8 + - - +
414D ALA* 1.3 79.6 - - - +
416D MET* 1.3 64.2 + - + +
417D GLN 3.4 0.7 + - - -
418D GLY* 4.5 3.5 + - - -
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Residues in contact with MET 416 (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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154D ASP* 4.6 9.9 - - + -
155D ARG* 3.9 37.2 - - + +
156D PRO* 4.2 4.7 - - + -
379D ILE* 6.0 2.7 - - + -
384D THR* 4.0 22.7 - - + -
412D ILE* 2.8 35.9 + - + +
413D ASP* 4.0 6.5 - - - +
415D ILE* 1.3 72.8 - - + +
417D GLN* 1.3 61.0 + - - +
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Residues in contact with GLN 417 (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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413D ASP* 2.9 19.6 + - + +
415D ILE 4.5 0.9 - - - -
416D MET* 1.3 81.6 - - - +
418D GLY* 1.3 59.2 + - - +
419D ILE* 3.3 18.8 - - + -
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Residues in contact with GLY 418 (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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414D ALA 3.0 8.1 + - - -
415D ILE 5.0 2.5 - - - -
417D GLN* 1.3 76.5 - - - +
419D ILE* 1.3 66.9 + - - +
420D PRO* 3.3 12.1 - - - +
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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
------------------------------------------------------------
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