Contacts of the helix formed by residues 74 - 86 (chain J) in PDB entry 6K71
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 ALA 74 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67J LEU* 4.4 15.0 - - + -
68J LEU 4.8 0.7 - - - +
69J PRO* 4.4 8.9 - - - +
73J VAL* 1.3 75.8 - - - +
75J LEU* 1.3 60.4 + - - +
76J ILE* 3.2 13.7 - - + -
77J ASP* 2.9 31.2 + - - +
78J TYR* 3.5 5.4 + - - -
105J HIS* 3.4 34.8 - - + +
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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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65J ARG* 5.5 0.9 - - - +
66J VAL* 3.4 17.2 + - + +
68J LEU* 3.5 41.6 + - + +
70J LEU* 5.0 13.0 - - + -
73J VAL 3.6 1.6 + - - -
74J ALA* 1.3 70.0 - - - +
76J ILE* 1.3 63.4 + - - +
78J TYR* 3.1 21.2 + - + +
79J THR* 3.0 23.1 + - + +
153J GLY 3.3 26.7 - - - +
154J ASP* 3.8 22.4 - - - +
155J VAL 4.8 2.5 - - - +
156J ILE* 5.9 4.5 - - + -
300J VAL* 3.7 22.9 - - + -
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Residues in contact with ILE 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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47J LEU* 6.1 3.4 - - + -
66J VAL* 3.6 40.6 + - + +
67J LEU* 4.3 8.5 - - + -
74J ALA* 3.8 12.6 - - + -
75J LEU* 1.3 78.1 - - - +
77J ASP* 1.3 68.8 + - - +
79J THR* 3.4 10.1 - - + +
80J LEU* 2.8 39.2 + - + +
93J VAL* 5.9 7.0 - - + -
102J ILE* 5.4 2.0 - - + -
105J HIS* 3.5 28.9 - - + +
106J LEU* 3.7 24.9 - - + -
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Residues in contact with ASP 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 VAL* 4.8 4.5 - - + +
74J ALA* 2.9 27.7 + - - +
76J ILE* 1.3 89.8 - - - +
78J TYR* 1.3 65.7 + - + +
80J LEU* 4.2 1.4 - - - +
81J GLU* 2.8 43.5 + - - +
105J HIS* 4.0 8.9 + - - -
106J LEU* 5.9 0.7 - - - +
109J SER* 5.4 1.5 - - - -
111J TRP* 3.2 29.2 - - + -
327J PHE* 5.4 9.0 - - + +
328J THR* 4.0 19.8 + - - +
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Residues in contact with TYR 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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70J LEU* 3.7 37.8 - - + +
71J ALA* 3.4 27.6 + - - +
73J VAL* 3.5 32.0 - - + +
74J ALA 3.5 1.9 + - - -
75J LEU* 3.1 23.6 + - + +
77J ASP* 1.3 81.6 - - + +
79J THR* 1.3 57.2 + - - +
81J GLU* 3.7 1.6 - - - +
82J PHE 2.9 22.3 + - - -
156J ILE* 3.3 38.8 - - + +
313J VAL* 5.4 6.5 - - + -
321J LEU* 4.5 15.2 - - + +
323J PRO* 3.6 11.9 - - + +
327J PHE* 4.2 22.2 - + - -
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Residues in contact with THR 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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47J LEU* 4.2 16.2 - - + +
75J LEU* 3.0 14.7 + - - +
76J ILE* 3.4 15.5 - - - +
78J TYR* 1.3 77.2 - - - +
80J LEU* 1.3 60.6 + - + +
82J PHE* 3.2 8.0 + - - +
83J LEU* 3.0 31.4 + - - +
151J VAL* 5.2 1.2 - - - +
152J TYR 3.8 13.7 + - - -
153J GLY* 3.6 28.7 - - - +
155J VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 80 (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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47J LEU* 6.2 4.0 - - + -
76J ILE* 2.8 27.4 + - + +
77J ASP* 4.2 1.1 - - - +
79J THR* 1.3 78.7 - - + +
81J GLU* 1.3 83.4 + - - +
83J LEU* 3.3 8.3 + - + +
84J THR* 2.8 37.4 + - - +
91J THR* 5.6 8.7 - - + -
93J VAL* 5.9 5.2 - - + -
106J LEU* 5.4 4.5 - - + -
111J TRP* 3.4 43.7 - - + +
118J ASN* 4.3 8.1 - - - +
120J VAL* 3.9 18.2 - - + -
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Residues in contact with GLU 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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77J ASP* 2.8 30.4 + - - +
78J TYR 3.7 2.5 - - - +
80J LEU* 1.3 93.9 - - - +
82J PHE* 1.3 60.8 + - - +
84J THR* 3.8 16.9 + - + +
85J ALA* 2.9 26.2 + - - +
111J TRP* 3.1 39.5 - - - -
321J LEU* 4.7 13.9 - - + +
327J PHE* 4.5 29.5 - - + +
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Residues in contact with PHE 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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78J TYR 2.9 13.9 + - - +
79J THR* 3.2 14.3 + - - +
81J GLU* 1.3 78.5 - - - +
83J LEU* 1.3 83.3 + - + +
85J ALA* 3.1 18.4 + - + +
86J THR* 3.3 20.6 + - + +
149J LEU* 5.3 5.6 - - + -
151J VAL* 4.7 4.3 - - + -
155J VAL* 4.9 8.1 - - + +
156J ILE* 4.6 5.3 - - + +
157J SER* 3.7 36.3 - - - +
158J ASN* 4.4 2.2 - - - -
159J ILE* 3.2 39.3 - - + -
161J ILE* 5.2 4.5 - - + -
249J ILE* 3.6 33.0 - - + -
321J LEU* 5.2 2.2 - - - -
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Residues in contact with LEU 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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45J ALA* 3.8 20.6 - - + -
47J LEU* 5.0 6.7 - - + -
79J THR* 3.0 17.8 + - - +
80J LEU* 3.3 10.5 + - - +
82J PHE* 1.3 98.7 - - + +
84J THR* 1.3 58.7 + - - +
85J ALA 3.4 0.2 - - - -
86J THR* 2.9 16.2 - - + +
88J VAL* 3.8 25.8 + - + +
91J THR* 4.7 19.3 - - + +
118J ASN* 5.1 1.3 - - - +
149J LEU* 3.7 26.0 - - + -
151J VAL* 3.8 25.8 - - + -
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Residues in contact with THR 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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20D GLU* 4.2 23.4 - - + +
80J LEU* 2.8 20.8 + - - +
81J GLU* 3.8 18.6 + - + +
83J LEU* 1.3 72.9 - - - +
85J ALA* 1.3 64.3 + - - +
86J THR 3.0 10.7 - - - +
87J GLY* 4.8 1.0 - - - -
116J SER* 6.5 0.9 - - - -
117J LEU* 3.8 28.1 - - + +
118J ASN* 2.4 35.1 + - - +
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Residues in contact with ALA 85 (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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20D GLU* 5.6 1.8 - - - -
24D ARG* 4.6 20.8 + - + +
81J GLU 2.9 22.1 + - - +
82J PHE* 3.1 15.0 + - + +
84J THR* 1.3 78.5 - - - +
86J THR* 1.3 60.9 + - - +
87J GLY 4.0 0.2 + - - -
158J ASN* 6.4 1.3 - - - -
159J ILE 6.2 0.2 - - - +
160J ASN* 4.1 12.3 - - - +
320J PRO* 6.3 3.1 - - + -
321J LEU* 5.2 9.4 - - + -
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Residues in contact with THR 86 (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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43J LEU* 5.4 2.3 - - + +
82J PHE* 3.3 16.9 + - + +
83J LEU* 2.9 26.8 - - - +
84J THR 3.0 9.9 - - - +
85J ALA* 1.3 79.3 - - - +
87J GLY* 1.3 63.3 + - - +
88J VAL* 3.3 6.9 + - + -
149J LEU* 4.4 13.9 - - + -
159J ILE 4.5 7.1 + - - +
160J ASN* 4.3 9.2 + - - +
161J ILE* 3.3 46.0 + - + +
162J THR* 4.4 7.6 + - - +
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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