Contacts of the helix formed by residues 76 - 82 (chain K) in PDB entry 6D6Q
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 GLN 76 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K VAL* 2.7 27.2 + - + +
75K HIS* 1.3 84.5 - - + +
77K ILE* 1.3 64.2 + - - +
78K ASP* 3.0 3.6 - - - +
79K VAL* 2.8 45.9 + - + +
80K LEU* 3.3 7.9 + - - +
176K ASN* 4.6 14.9 + - - +
194K CYS* 2.8 47.6 - - - +
195K GLU* 5.1 1.4 - - - +
211K LEU* 4.0 21.3 - - + +
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Residues in contact with ILE 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K VAL 3.8 2.6 + - - -
73K LEU* 3.6 14.5 + - - +
74K LEU 5.8 1.6 - - - +
75K HIS 3.8 1.3 - - - -
76K GLN* 1.3 77.7 - - - +
78K ASP* 1.3 56.3 + - + +
80K LEU* 2.9 11.2 + - + +
81K GLU* 2.5 45.9 + - + +
105K VAL* 3.8 17.3 - - + +
108K ARG* 3.5 54.7 - - + +
109K ILE* 3.4 37.0 - - + -
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Residues in contact with ASP 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76K GLN* 3.0 1.7 - - - -
77K ILE* 1.3 82.2 - - + +
79K VAL* 1.3 61.9 + - + +
80K LEU 3.0 5.3 + - - -
81K GLU* 4.0 12.9 - - - +
82K ASP* 3.2 18.7 + - - +
210K ARG* 3.4 55.2 + - - +
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Residues in contact with VAL 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K VAL* 6.4 0.2 - - + -
76K GLN* 2.8 47.2 + - + +
78K ASP* 1.3 77.3 - - + +
80K LEU* 1.3 61.6 + - + +
82K ASP* 2.7 29.9 - - - +
85K ILE* 4.3 5.6 - - + +
194K CYS* 5.7 2.2 - - + -
197K TYR* 6.5 1.3 - - + -
198K VAL* 4.9 20.6 - - + -
207K LEU* 4.7 14.8 - - + +
210K ARG* 5.6 2.7 - - - +
211K LEU* 4.6 20.9 - - + +
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Residues in contact with LEU 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K LEU* 5.5 9.4 - - + -
68K PRO* 4.5 8.1 - - + -
72K VAL* 4.3 22.2 - - + +
73K LEU* 4.1 29.2 - - + -
76K GLN 3.9 10.3 - - - +
77K ILE* 2.9 12.0 + - + +
79K VAL* 1.3 89.5 - - + +
81K GLU* 1.3 63.0 + - - +
82K ASP* 2.9 18.5 - - - +
85K ILE* 3.8 12.1 - - + +
88K VAL* 5.2 15.0 - - + -
109K ILE* 5.6 1.6 - - + -
118K LYS* 4.9 0.5 - - - +
120K PHE* 3.5 32.6 - - + -
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Residues in contact with GLU 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ILE* 2.5 29.1 + - + +
78K ASP* 4.0 12.6 - - - +
80K LEU* 1.3 71.6 - - - +
82K ASP* 1.3 60.7 - - - +
83K PRO* 3.6 2.8 - - - +
108K ARG* 4.5 12.3 - - - +
112K VAL* 2.9 32.1 - - - +
118K LYS* 3.5 29.6 + - - +
120K PHE* 5.1 2.0 - - - -
210K ARG* 5.0 0.2 - - - -
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Residues in contact with ASP 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K ASP 3.2 10.8 + - - +
79K VAL* 2.7 33.1 - - - +
80K LEU* 2.9 16.2 - - - +
81K GLU* 1.3 74.3 - - - +
83K PRO* 1.3 65.4 - - + +
84K ALA* 4.2 4.9 - - + +
85K ILE* 3.4 22.2 - - - +
118K LYS* 4.2 3.5 - - - +
207K LEU* 3.0 31.2 - - + +
210K ARG* 3.0 27.8 - - - +
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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