Contacts of the helix formed by residues 410 - 416 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C HIS* 3.6 20.8 + - - +
63C LEU* 3.8 21.2 + - - +
64C SER* 3.7 9.1 + - - +
85C VAL* 4.5 6.7 - - + +
86C LEU 3.1 20.9 + - - +
87C SER* 4.7 2.3 + - - +
92C ILE* 4.3 4.8 - - - +
383C PRO 3.8 0.7 - - - +
384C PHE* 3.7 23.4 - - + -
408C PHE 4.1 0.8 - - - -
409C VAL* 1.3 68.6 - - - +
411C GLN* 1.3 60.6 + - - +
412C TRP* 3.0 12.6 + - - +
413C GLN* 2.7 44.9 + - + +
414C ILE* 3.8 9.0 + - - +
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Residues in contact with GLN 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C VAL* 2.9 24.7 + - - +
383C PRO 2.8 10.3 + - - +
385C THR* 3.8 22.9 - - + +
409C VAL* 3.3 5.8 + - + +
410C ASN* 1.3 70.3 - - - +
412C TRP* 1.3 66.2 + - - +
414C ILE* 3.1 20.7 + - + +
415C ASN* 3.2 19.4 + - - +
448C ILE* 3.9 19.9 - - + +
449C ILE* 3.3 31.3 + - - +
451C GLY* 2.9 36.2 + - - -
601C HEM 3.8 9.3 - - - +
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Residues in contact with TRP 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C HIS* 3.5 33.1 + + + -
61C LEU* 3.3 26.7 - - + -
64C SER* 3.2 35.2 - - - -
378C HIS 4.9 0.8 + - - -
379C SER 4.3 5.7 + - - -
380C SER* 3.3 37.1 - - - -
383C PRO* 3.0 23.1 + - + +
410C ASN* 3.0 7.4 + - - +
411C GLN* 1.3 77.7 - - - +
413C GLN* 1.3 61.3 - - - +
415C ASN 3.4 1.0 + - - -
416C HIS* 3.2 62.0 + + + -
492C PRO* 6.2 0.8 - - - +
498C MET* 4.3 3.2 - - + +
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Residues in contact with GLN 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C SER* 3.6 22.4 + - - +
67C SER* 3.8 22.3 + - - +
68C GLN* 6.1 1.8 - - - +
72C ASP* 5.7 1.2 + - - -
87C SER* 3.9 8.9 - - - +
88C GLY* 2.9 32.6 + - - +
410C ASN* 2.7 33.6 + - + +
411C GLN 3.1 0.6 - - - -
412C TRP* 1.3 77.0 - - - +
414C ILE* 1.3 67.5 + - - +
416C HIS 3.6 1.4 - - - -
417C ASP* 3.0 47.7 + - - +
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Residues in contact with ILE 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLY 4.0 17.0 - - - +
89C LEU* 4.1 14.6 - - + +
92C ILE* 3.6 29.6 - - + -
410C ASN 4.2 7.6 - - - +
411C GLN* 3.1 9.3 + - + +
413C GLN* 1.3 87.1 - - - +
415C ASN* 1.3 61.5 + - - +
416C HIS 3.0 6.5 + - - -
417C ASP* 3.1 14.5 + - - +
420C LEU* 4.2 11.4 - - + +
421C TRP* 3.1 14.4 + - - -
446C LYS 3.7 23.3 - - - +
448C ILE* 3.8 33.0 - - + -
452C MET* 5.3 0.2 - - + -
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Residues in contact with ASN 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C PHE 4.1 7.7 + - - -
377C ARG* 2.9 48.2 + - + +
380C SER* 3.0 33.2 + - - +
411C GLN* 3.2 14.4 + - - +
412C TRP 4.1 1.1 - - - +
414C ILE* 1.3 77.3 - - - +
416C HIS* 1.3 59.2 + - - +
421C TRP* 3.4 10.4 + - - +
446C LYS 4.1 0.2 - - - +
447C VAL* 3.8 7.8 - - - -
448C ILE* 2.7 45.3 + - - +
449C ILE* 4.5 3.6 - - - +
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Residues in contact with HIS 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C ARG* 3.4 7.3 + - - -
378C HIS* 3.1 38.1 + + - -
380C SER* 3.8 7.7 + - - -
412C TRP* 3.2 68.3 + + + +
413C GLN* 3.6 2.2 - - - +
414C ILE 3.0 0.6 - - - -
415C ASN* 1.3 80.3 - - - +
417C ASP* 1.3 66.0 + - - +
418C GLN* 3.3 4.5 + - - +
424C PRO* 3.5 43.9 + - + +
425C SER* 4.8 4.8 + - - -
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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
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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