Contacts of the helix formed by residues 70 - 84 (chain J) in PDB entry 5G04
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 GLU 70 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65J LEU 5.0 0.2 + - - -
66J ASP 3.3 9.4 + - - -
67J LYS 4.7 0.6 + - - -
69J TYR* 1.3 80.7 - - - +
71J ALA* 1.3 64.6 + - - +
72J CYS 3.3 2.7 - - - +
73J ARG* 3.2 49.6 + - - +
74J TYR* 3.1 20.6 + - - +
128J ILE* 5.2 7.0 - - + +
129J LYS* 5.0 13.3 - - - +
132J ILE* 4.5 16.4 - - + +
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Residues in contact with ALA 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J TYR* 4.1 15.5 + - + -
69J TYR* 3.4 9.3 + - + -
70J GLU* 1.3 76.6 - - - +
72J CYS* 1.3 64.7 + - - +
74J TYR* 3.4 19.4 + - - +
75J LEU* 3.5 3.8 + - - +
128J ILE* 4.5 27.8 - - + +
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Residues in contact with CYS 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J PRO 4.4 3.8 - - - -
41J TYR* 3.7 33.2 - - - -
60J LEU* 3.7 18.3 - - + +
65J LEU* 4.0 27.8 - - - +
66J ASP* 4.1 17.9 - - - +
69J TYR* 4.6 11.6 - - + +
70J GLU 4.3 0.6 - - - +
71J ALA* 1.3 81.2 - - - +
73J ARG* 1.3 65.3 + - - +
75J LEU* 3.1 4.4 + - - +
76J ALA* 3.0 23.4 + - - +
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Residues in contact with ARG 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J ASP* 3.6 30.0 + - + +
67J LYS* 4.5 15.8 + - - +
70J GLU* 3.2 47.0 + - - +
72J CYS* 1.3 77.0 - - - +
74J TYR* 1.3 64.2 + - - +
76J ALA* 3.3 1.7 + - - -
77J ALA* 3.0 22.3 + - - +
92J VAL* 3.6 33.7 + - + +
93J LEU* 3.8 19.4 + - + +
95J MET* 4.7 18.2 + - - +
132J ILE* 4.1 19.5 - - + +
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Residues in contact with TYR 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 5.5 5.2 - - - -
70J GLU 3.1 12.1 + - - +
71J ALA* 3.4 13.0 - - - +
72J CYS 3.2 0.2 - - - -
73J ARG* 1.3 76.3 - - - +
75J LEU* 1.3 62.4 + - + +
77J ALA* 3.2 6.5 + - - +
78J ARG* 2.8 72.6 + - - +
128J ILE* 5.1 9.2 - - + -
131J SER* 4.1 16.3 + - - -
132J ILE* 3.9 33.0 - - + -
134J LEU* 5.8 1.6 - - - +
135J LEU* 3.6 34.5 - - + +
16K GLN 4.3 12.6 - - - -
17K GLN* 5.1 2.9 - - - -
18K GLN* 3.5 16.3 + - - -
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Residues in contact with LEU 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J TYR* 3.6 36.3 - - + +
44J ALA* 3.7 14.8 - - + -
45J GLN* 3.6 38.6 - - - +
48J TYR* 4.0 30.7 - - + -
56J ALA* 5.9 1.3 - - + -
60J LEU* 3.8 8.1 - - + -
71J ALA 3.5 1.8 + - - +
72J CYS 3.1 8.6 + - - +
74J TYR* 1.3 84.9 - - + +
76J ALA* 1.3 56.6 + - - +
78J ARG* 3.1 8.0 + - + +
79J CYS* 2.9 27.5 + - + +
17K GLN* 4.5 9.9 - - - +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ALA* 5.1 4.9 - - - +
60J LEU* 3.7 23.2 - - + +
61J ARG* 4.6 18.4 - - - -
66J ASP* 4.7 5.2 - - + -
72J CYS 3.0 15.8 + - - +
73J ARG* 3.7 7.0 - - - +
75J LEU* 1.3 75.4 - - - +
77J ALA* 1.3 63.2 + - - +
79J CYS* 3.1 8.3 + - - +
80J HIS* 3.0 29.5 + - - -
92J VAL* 4.6 8.1 - - + -
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Residues in contact with ALA 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J ARG 3.0 12.7 + - - +
74J TYR* 3.4 10.8 - - - +
76J ALA* 1.3 75.4 - - - +
78J ARG* 1.3 63.8 + - - +
80J HIS 3.2 1.4 + - - -
81J TYR* 3.0 22.5 + - - +
89J ALA* 3.7 13.8 - - + +
92J VAL* 3.9 11.1 - - + +
93J LEU* 3.1 36.8 - - + -
135J LEU* 3.8 11.3 - - + +
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Residues in contact with ARG 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J TYR* 3.0 30.6 + - + +
74J TYR* 2.8 53.9 + - + +
75J LEU* 3.1 13.9 + - + +
77J ALA* 1.3 79.3 - - - +
79J CYS* 1.3 56.1 + - - +
81J TYR* 3.3 9.2 + - + +
82J ALA* 2.9 27.5 + - - +
135J LEU* 3.7 17.0 - - + +
16K GLN 4.2 0.2 + - - -
17K GLN* 2.9 66.1 + - - +
18K GLN* 4.3 3.4 + - - +
19K TYR* 4.4 11.5 - - - +
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Residues in contact with CYS 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J TYR* 4.0 13.9 - - + -
53J TYR* 2.6 51.2 - - - +
56J ALA* 3.5 11.4 - - + -
57J ALA* 3.5 17.9 - - + +
60J LEU* 6.2 0.2 - - + -
75J LEU* 2.9 13.6 + - + +
76J ALA* 3.1 13.2 + - - +
78J ARG* 1.3 77.3 - - - +
80J HIS* 1.3 57.9 + - - +
82J ALA* 3.3 3.3 + - - +
83J ALA* 3.0 27.6 + - - +
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Residues in contact with HIS 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J HIS* 5.4 9.9 + - - -
57J ALA* 3.6 27.3 - - + +
61J ARG* 3.7 30.4 + - - -
76J ALA 3.0 23.0 + - - +
77J ALA 3.2 2.7 + - - +
79J CYS* 1.3 75.4 - - - +
81J TYR* 1.3 55.2 + - - +
83J ALA* 3.1 7.0 + - + +
84J LYS 3.0 7.4 + - - -
85J GLU* 2.8 57.6 + - + -
88J GLN* 4.0 19.3 + - + -
89J ALA* 3.7 28.0 - - + +
92J VAL* 4.7 5.3 - - - +
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Residues in contact with TYR 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J TYR* 5.8 1.3 - - - -
77J ALA 3.0 13.1 + - - +
78J ARG* 3.5 14.4 - - + +
79J CYS 3.2 0.2 - - - -
80J HIS* 1.3 75.5 - - - +
82J ALA* 1.3 64.5 - - + +
84J LYS* 2.9 35.0 + - - +
86J HIS* 3.4 37.3 - + - -
89J ALA* 4.1 2.8 - - + +
135J LEU* 4.0 19.3 - - + -
138J LYS* 3.7 56.4 + - + +
139J ILE* 3.8 16.6 - - + -
142J ALA* 4.5 4.0 - - + +
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Residues in contact with ALA 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J TYR* 3.7 15.0 - - + +
53J TYR* 3.6 42.1 - - + +
78J ARG 2.9 17.1 + - - +
79J CYS 3.7 2.5 - - - +
81J TYR* 1.3 81.9 - - + +
83J ALA* 1.3 60.4 + - - +
84J LYS* 3.4 8.6 + - - +
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Residues in contact with ALA 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J TYR* 4.3 17.7 - - + -
54J HIS* 5.5 4.5 - - - +
79J CYS 3.0 13.0 + - - +
80J HIS* 3.3 14.1 - - + +
81J TYR 3.1 0.2 - - - -
82J ALA* 1.3 77.0 - - - +
84J LYS* 1.3 69.4 + - - +
85J GLU* 4.0 17.8 - - + +
294K LEU* 5.7 9.2 - - + -
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Residues in contact with LYS 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J TYR* 2.9 33.3 + - - +
82J ALA* 4.2 7.2 - - - +
83J ALA* 1.3 81.9 - - - +
85J GLU* 1.3 61.1 + - - +
86J HIS* 3.3 47.6 + - + +
142J ALA* 4.7 5.3 - - - +
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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