Contacts of the helix formed by residues 358 - 364 (chain C) in PDB entry 6DWN
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 ARG 358 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C THR* 3.3 23.6 + - - -
156C SER* 2.3 32.5 + - - +
160C GLU* 2.9 28.9 + - - +
161C GLU* 5.6 1.6 + - - -
355C ARG* 4.6 9.0 - - - +
356C ARG* 3.9 11.1 - - + +
357C PRO* 1.3 81.8 - - - +
359C LEU* 1.3 65.8 + - - +
360C SER* 3.2 16.7 + - - +
361C ASP* 2.9 25.5 + - - +
362C ARG 3.7 2.1 + - - -
468C PHE* 3.8 9.9 - - - -
469C LEU* 4.5 2.2 - - - -
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Residues in contact with LEU 359 (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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157C CYS* 4.0 19.1 - - - -
159C LEU* 5.3 2.2 - - + -
160C GLU* 3.0 28.8 + - + +
358C ARG* 1.3 71.5 - - - +
360C SER* 1.3 56.1 + - - +
362C ARG* 2.8 30.4 + - + +
363C SER 4.5 0.3 + - - -
465C TRP* 3.3 54.3 - - + -
468C PHE* 4.5 9.6 - - + -
469C LEU* 3.3 39.0 - - + -
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Residues in contact with SER 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C ARG* 5.8 0.2 + - - -
358C ARG* 3.9 16.3 + - - +
359C LEU* 1.3 78.3 - - - +
361C ASP* 1.3 69.7 + - - +
362C ARG 3.6 0.5 + - - -
363C SER* 4.1 9.2 + - - -
364C HIS* 4.3 12.8 - - - -
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Residues in contact with ASP 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C VAL* 5.8 0.7 - - + -
351C ILE* 3.3 23.8 - - + +
355C ARG* 3.1 40.2 + - - -
358C ARG* 2.9 24.4 + - - +
360C SER* 1.3 82.5 + - - +
362C ARG* 1.3 55.0 + - - +
363C SER 3.1 3.8 - - - -
364C HIS* 2.7 41.2 + - + +
365C LEU* 2.8 20.2 - - + +
468C PHE* 5.0 1.8 - - + -
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Residues in contact with ARG 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C ARG 3.7 1.8 + - - -
359C LEU* 2.8 19.3 + - - +
361C ASP* 1.3 77.1 - - - +
363C SER* 1.3 61.3 + - - +
364C HIS 3.2 1.2 + - - -
365C LEU* 3.4 15.9 + - - +
369C GLU* 3.8 35.6 + - + +
464C ARG* 4.1 32.3 + - - +
465C TRP* 3.7 36.5 - - - +
468C PHE* 3.6 43.8 - - + +
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Residues in contact with SER 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU 4.5 0.2 + - - -
360C SER 4.1 7.0 + - - -
361C ASP 3.1 1.0 - - - -
362C ARG* 1.3 78.6 - - - +
364C HIS* 1.3 74.9 + - - +
365C LEU 3.5 1.1 + - - -
366C PRO* 5.2 2.6 - - - +
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Residues in contact with HIS 364 (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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350C VAL* 3.7 33.9 - - + +
360C SER 4.3 11.6 + - - -
361C ASP* 2.7 29.7 + - - +
363C SER* 1.3 90.4 + - - +
365C LEU* 1.3 59.3 + - - +
366C PRO* 3.3 15.0 - - - +
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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