Contacts of the helix formed by residues 74 - 83 (chain K) in PDB entry 4G7Z
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 ASP 74 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66K SER 4.5 3.6 - - - +
67K THR* 4.6 8.3 - - - -
72K LYS 3.7 2.2 + - - -
73K GLU* 1.3 78.2 - - - +
75K VAL* 1.3 66.4 + - - +
76K VAL* 3.6 10.2 + - - +
77K GLU* 2.8 45.7 + - - +
78K ILE* 3.2 9.5 + - - +
627M ARG* 3.0 42.1 + - - +
628M PHE* 4.3 16.2 - - + -
640M ARG* 3.3 23.5 + - - -
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Residues in contact with VAL 75 (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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58K ILE* 5.2 7.6 - - + -
61K VAL* 3.8 24.0 - - + -
63K HIS 4.3 0.2 - - - +
64K GLU* 3.3 33.7 - - - +
66K SER* 3.3 28.2 + - - +
67K THR* 4.1 4.5 - - - +
68K ILE* 4.4 10.3 - - + -
73K GLU 4.0 0.2 + - - -
74K ASP* 1.3 73.0 - - - +
76K VAL* 1.3 61.3 + - - +
78K ILE* 3.9 8.7 - - + +
79K ILE* 3.0 32.1 + - + +
165K ILE* 3.9 16.4 - - + -
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Residues in contact with VAL 76 (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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64K GLU* 3.6 36.6 + - + +
65K PHE* 5.2 2.0 - - + -
66K SER 5.1 0.2 + - - -
74K ASP* 3.1 13.1 - - - +
75K VAL* 1.3 79.8 - - - +
77K GLU* 1.3 59.3 + - - +
79K ILE* 3.9 1.4 - - - +
80K LEU* 3.0 43.0 + - + +
572M ILE* 4.8 14.4 - - + +
628M PHE* 4.9 7.8 - - + -
640M ARG* 4.2 19.7 - - - +
703M ILE* 4.3 23.6 - - + -
830M LYS* 5.5 4.0 - - + -
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Residues in contact with GLU 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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73K GLU* 3.5 33.2 - - + +
74K ASP* 2.8 24.2 + - - +
76K VAL* 1.3 76.7 - - - +
78K ILE* 1.3 59.9 + - - +
80K LEU* 3.5 9.6 + - + +
81K ASN* 2.9 40.6 + - - +
640M ARG* 3.8 23.6 + - - +
642M ARG* 4.6 11.6 + - - -
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Residues in contact with ILE 78 (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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58K ILE* 5.3 7.2 - - + -
68K ILE* 4.7 14.8 - - + -
71K VAL* 4.1 17.9 - - + -
73K GLU* 3.6 23.3 - - + +
74K ASP 3.2 6.7 + - - +
75K VAL* 3.9 9.6 - - + +
76K VAL 3.4 0.2 - - - -
77K GLU* 1.3 74.5 - - - +
79K ILE* 1.3 56.8 + - + +
80K LEU 3.1 1.1 - - - -
81K ASN* 2.9 7.7 + - - +
82K LEU* 2.7 48.4 + - + +
129K ILE* 4.1 17.7 - - + +
130K ALA* 3.7 25.4 - - + -
138K LEU* 4.8 7.0 - - + -
140K MET* 4.8 9.0 - - - -
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Residues in contact with ILE 79 (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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56K VAL* 3.6 40.2 - - + -
58K ILE* 6.1 0.7 - - + -
64K GLU* 4.1 24.7 - - + +
75K VAL* 3.0 34.5 + - + +
76K VAL 3.9 4.0 - - - +
78K ILE* 1.3 75.1 - - + +
80K LEU* 1.3 63.8 + - + +
82K LEU* 3.2 8.3 + - + +
83K LYS* 3.1 28.0 + - + +
165K ILE* 4.3 14.1 - - + -
167K VAL* 3.6 32.2 - - + +
830M LYS* 6.2 0.4 - - - +
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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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64K GLU* 5.2 4.7 - - - +
76K VAL* 3.0 36.8 + - + +
77K GLU* 3.6 11.2 - - + +
78K ILE 3.1 0.2 - - - -
79K ILE* 1.3 82.5 - - + +
81K ASN* 1.3 62.6 + - - +
82K LEU 3.4 0.2 - - - -
83K LYS* 3.6 22.4 - - + +
84K GLU* 4.1 11.1 - - - +
572M ILE* 4.7 8.5 - - + -
573M ARG* 3.6 42.6 - - + +
697M ARG 5.6 0.7 - - - +
698M ASP* 3.7 27.1 - - + +
830M LYS* 6.3 1.6 - - + +
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Residues in contact with ASN 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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73K GLU* 4.0 13.3 + - - +
77K GLU* 2.9 33.4 + - - +
78K ILE 2.9 6.4 + - - +
80K LEU* 1.3 80.5 - - - +
82K LEU* 1.3 61.1 + - - +
83K LYS 3.2 0.9 - - - -
84K GLU* 3.5 13.9 + - - +
127K LEU* 3.6 23.4 - - - +
128K HIS* 3.7 22.2 + - - +
129K ILE* 2.8 31.2 + - - +
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Residues in contact with LEU 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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53K VAL* 3.4 23.7 + - + +
56K VAL* 3.6 39.5 - - + -
78K ILE* 2.7 36.1 + - + +
79K ILE* 3.2 10.7 + - + +
81K ASN* 1.3 69.6 - - - +
83K LYS* 1.3 64.1 + - - +
84K GLU 3.1 2.0 - - - -
85K LEU* 3.3 27.7 + - + +
114K PHE* 4.3 24.9 - - + -
127K LEU* 5.5 0.4 - - + -
129K ILE* 4.5 20.0 - - + -
140K MET* 4.5 7.0 - - + -
142K VAL* 4.4 10.8 - - + -
167K VAL* 5.8 1.3 - - + -
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Residues in contact with LYS 83 (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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52K ALA* 5.7 4.7 - - - +
53K VAL* 5.5 3.2 + - - +
79K ILE* 3.1 13.4 + - + +
80K LEU* 3.6 22.4 - - + +
81K ASN 3.2 0.2 - - - -
82K LEU* 1.3 78.8 - - - +
84K GLU* 1.3 61.8 + - + +
85K LEU 3.2 7.3 + - - +
150K TYR* 5.2 0.2 - - - -
167K VAL* 4.2 8.5 - - + -
168K ASP* 3.3 51.4 + - - +
170K VAL* 5.1 13.9 - - + +
175K ARG* 5.7 1.4 + - - -
695M LEU 4.6 1.6 + - - -
696M LYS 2.9 26.6 + - - +
697M ARG* 4.8 2.9 - - - -
698M ASP* 2.9 30.4 + - + +
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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