Contacts of the helix formed by residues 410 - 416 (chain D) in PDB entry 6DWM
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 ASN 410 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D HIS* 3.6 20.4 + - - +
63D LEU* 3.9 20.6 + - - +
64D SER* 3.6 9.5 + - - +
85D VAL* 4.7 4.5 - - + +
86D LEU 3.1 18.4 + - - +
87D SER* 4.6 5.9 + - - +
92D ILE* 4.2 5.4 - - - +
383D PRO 3.9 0.9 - - - +
384D PHE* 3.7 21.3 - - + -
408D PHE 4.0 0.6 - - - -
409D VAL* 1.3 69.5 - - - +
411D GLN* 1.3 60.4 + - - +
412D TRP* 3.1 13.0 + - - +
413D GLN* 2.7 44.5 + - + +
414D ILE* 3.8 11.6 + - - +
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Residues in contact with GLN 411 (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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380D SER* 5.3 0.2 - - - -
382D VAL* 2.7 38.2 + - - +
383D PRO 2.8 9.9 + - - +
384D PHE 4.4 1.0 - - - -
385D THR* 3.8 22.8 - - + +
409D VAL* 3.3 6.0 + - + +
410D ASN* 1.3 71.8 - - - +
412D TRP* 1.3 66.3 + - - +
414D ILE* 3.2 19.5 + - + +
415D ASN* 3.2 19.1 + - - +
448D ILE* 3.5 21.4 - - + +
449D ILE* 3.1 31.9 + - - +
451D GLY* 3.0 34.0 + - - -
601D HEM 3.9 1.7 - - - +
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Residues in contact with TRP 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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60D HIS* 3.6 28.5 + + + -
61D LEU* 3.2 28.3 - - + -
64D SER* 3.0 36.6 - - - -
378D HIS 4.8 0.4 + - - -
379D SER 4.3 6.9 + - - -
380D SER* 3.5 30.7 - - - -
383D PRO* 3.0 23.1 + - + +
410D ASN* 3.1 7.6 + - - +
411D GLN* 1.3 76.4 - - - +
413D GLN* 1.3 62.7 + - - +
414D ILE 3.3 0.2 + - - -
415D ASN 3.3 1.2 + - - -
416D HIS* 3.1 61.9 + + + -
492D PRO* 6.1 1.2 - - - +
498D MET* 4.4 5.9 - - + +
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Residues in contact with GLN 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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64D SER* 3.7 20.2 + - - +
67D SER* 3.7 23.0 + - - +
68D GLN* 5.9 3.4 - - - +
72D ASP* 5.7 1.6 + - - -
87D SER* 4.1 7.6 - - - -
88D GLY* 3.2 28.3 + - - +
410D ASN* 2.7 34.9 + - + +
411D GLN 3.2 0.4 - - - -
412D TRP* 1.3 75.7 - - - +
414D ILE* 1.3 63.5 + - - +
416D HIS 3.5 1.3 + - - -
417D ASP* 2.9 57.7 + - - +
419D LYS* 5.5 3.8 - - - +
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Residues in contact with ILE 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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88D GLY 3.9 16.4 - - - +
89D LEU* 4.0 21.1 - - + +
92D ILE* 3.4 31.0 - - + -
410D ASN 3.8 7.6 + - - +
411D GLN* 3.2 9.3 + - + +
413D GLN* 1.3 88.2 - - - +
415D ASN* 1.3 62.2 + - - +
416D HIS 3.0 2.0 + - - -
417D ASP* 3.2 13.2 + - - +
420D LEU* 4.2 7.1 - - + +
421D TRP* 3.0 18.4 + - - -
446D LYS 3.5 23.3 - - - +
448D ILE* 3.9 30.7 - - + -
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Residues in contact with ASN 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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376D PHE 4.1 7.3 + - - -
377D ARG* 2.8 48.7 + - + +
380D SER* 3.0 32.7 + - - +
411D GLN* 3.2 11.7 + - - +
412D TRP 3.3 1.5 + - - +
414D ILE* 1.3 74.9 - - - +
416D HIS* 1.3 58.8 + - - +
421D TRP* 3.4 12.2 + - - +
446D LYS 3.9 2.8 - - - +
447D VAL* 3.5 9.8 - - - +
448D ILE 2.9 45.5 + - - +
449D ILE* 4.7 3.8 - - - +
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Residues in contact with HIS 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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377D ARG* 3.3 9.2 + - - -
378D HIS* 2.8 38.9 + + - -
380D SER* 3.8 7.7 + - - -
412D TRP* 3.1 69.5 + + + +
413D GLN 3.6 2.7 - - - +
414D ILE 3.1 0.4 - - - -
415D ASN* 1.3 80.1 + - - +
417D ASP* 1.3 66.3 + - - +
418D GLN* 3.3 4.7 + - - +
424D PRO* 3.4 44.3 + - + +
425D SER* 4.7 4.1 + - - -
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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
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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