Contacts of the helix formed by residues 72 - 86 (chain J) in PDB entry 2QJK
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 HIS 72 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70G THR* 4.3 18.2 - - + -
75G LEU* 3.9 32.2 - - + +
70J THR* 2.8 14.7 + - + -
71J PRO* 1.3 78.1 - - - +
73J VAL* 1.3 59.8 + - + +
74J ASP* 2.7 41.6 + - + +
75J LEU* 2.6 34.2 + - + +
76J ALA 3.0 8.1 + - - -
188J ASN* 3.3 27.4 + - - -
191J LEU* 3.7 7.2 - - - +
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Residues in contact with VAL 73 (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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72J HIS* 1.3 78.5 - - + +
74J ASP* 1.3 77.0 + - - +
75J LEU 3.3 1.6 + - - -
76J ALA* 4.1 5.6 + - - +
77J PHE* 4.7 3.8 + - - +
151J TRP* 3.4 54.1 - - + +
187J ASP* 4.4 6.3 - - - +
188J ASN* 2.9 40.4 + - + +
191J LEU* 3.4 10.9 - - + +
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Residues in contact with ASP 74 (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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72J HIS* 2.7 30.3 + - + +
73J VAL* 1.3 82.3 - - - +
75J LEU* 1.3 70.0 + - + +
78J ALA* 4.9 4.3 + - - +
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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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72G HIS* 4.0 25.4 - - + +
75G LEU* 3.6 27.8 - - + -
70J THR* 3.5 33.9 - - + -
72J HIS* 2.6 12.4 + - - +
74J ASP* 1.3 87.7 - - + +
76J ALA* 1.3 66.5 + - - +
77J PHE 3.2 2.0 - - - -
78J ALA* 2.7 26.5 + - + +
79J SER* 2.8 10.8 + - - +
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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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69J TYR* 3.8 18.3 - - - +
70J THR 3.0 21.3 + - - +
72J HIS 3.0 19.6 + - - +
73J VAL 4.2 2.9 - - - +
75J LEU* 1.3 73.7 - - - +
77J PHE* 1.3 60.0 + - - +
79J SER* 2.8 20.7 - - - -
80J VAL* 3.1 14.4 + - - +
149J LEU 3.9 7.9 - - - +
150J PRO 4.3 1.6 - - - -
151J TRP* 4.1 7.2 - - + -
191J LEU* 4.1 7.9 - - + -
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Residues in contact with PHE 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 4.7 4.5 + - - +
75J LEU 2.7 5.3 + - - -
76J ALA* 1.3 73.1 - - - +
78J ALA* 1.3 64.7 + - - +
80J VAL* 2.9 19.1 + - + +
81J GLU* 3.0 14.3 + - + +
94J ARG* 6.0 2.7 - - - -
150J PRO* 3.2 30.9 + - + +
151J TRP* 4.0 15.2 - - + +
152J GLY* 4.6 0.9 - - - -
279J ASN 3.7 20.4 - - - -
280J TYR* 3.9 19.7 - + - -
281J ILE 4.5 3.4 - - - -
282J GLU* 3.1 38.1 - - + +
44K PHE* 3.5 30.1 - + - -
102K LEU* 3.8 25.6 - - + -
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Residues in contact with ALA 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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74J ASP 4.9 3.4 - - - +
75J LEU* 2.7 22.1 + - + +
77J PHE* 1.3 73.6 - - - +
79J SER* 1.3 65.4 + - - +
81J GLU* 2.9 3.3 + - - +
82J HIS* 2.7 26.0 + - - +
44K PHE* 3.7 30.9 - - + -
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Residues in contact with SER 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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68J HIS 3.5 4.3 + - - +
69J TYR* 3.1 16.3 - - - -
70J THR* 2.7 37.1 + - - -
75J LEU* 2.8 11.2 + - - +
76J ALA* 2.8 23.8 + - - -
78J ALA* 1.3 76.4 - - - +
80J VAL* 1.3 55.4 + - - -
82J HIS* 3.1 24.8 - - - +
83J ILE* 3.1 14.8 + - - +
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Residues in contact with VAL 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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69J TYR* 3.9 24.0 - - + -
76J ALA 3.1 13.2 + - - +
77J PHE* 2.9 12.4 + - + +
79J SER* 1.3 73.8 - - - +
81J GLU* 1.3 68.2 + - - +
82J HIS 3.1 0.9 - - - -
83J ILE* 3.1 11.8 + - + +
84J MET* 3.0 20.1 + - + +
94J ARG* 3.3 48.0 - - + +
150J PRO* 4.1 16.2 - - + -
502J HEM 4.2 11.4 - - + +
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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 PHE* 3.0 15.1 + - + +
78J ALA 2.9 7.3 + - - +
80J VAL* 1.3 74.7 - - + +
82J HIS* 1.3 67.4 + - - +
84J MET* 2.9 21.6 + - - +
85J ARG* 2.7 73.2 + - - +
94J ARG* 5.0 1.6 + - - -
280J TYR* 4.6 9.7 - - - -
44K PHE* 4.3 24.2 - - + -
102K LEU* 3.6 38.5 - - + +
105K LYS* 4.7 3.3 + - - -
219K ALA 4.4 2.4 - - - +
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Residues in contact with HIS 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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68J HIS* 4.6 13.5 + - + -
78J ALA 2.7 11.9 + - - +
79J SER* 3.1 17.7 - - - +
81J GLU* 1.3 76.4 - - - +
83J ILE* 1.3 66.8 + - + +
85J ARG* 5.0 1.3 - - - +
86J ASN* 2.6 66.1 + - + +
87J VAL* 4.0 17.1 - - + +
41L SER* 4.5 4.7 + - - -
43L ASP* 3.5 33.8 - - - -
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Residues in contact with ILE 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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65J LEU* 3.6 41.7 - - + +
68J HIS* 3.6 37.2 - - + -
69J TYR* 4.2 7.4 - - + +
79J SER 3.1 15.2 + - - +
80J VAL* 3.1 14.8 + - + +
82J HIS* 1.3 78.1 - - + +
84J MET* 1.3 62.7 + - - +
87J VAL* 3.6 22.1 + - + +
90J GLY* 3.1 42.4 - - - +
93J LEU* 6.2 0.2 - - + -
94J ARG* 4.8 4.9 - - + -
502J HEM 5.1 5.6 - - + -
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Residues in contact with MET 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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80J VAL 3.0 17.2 + - - +
81J GLU* 2.9 30.7 + - - +
83J ILE* 1.3 80.9 - - - +
85J ARG* 1.3 60.8 + - + +
87J VAL 4.8 1.7 - - - +
91J PHE* 3.5 36.6 + - + +
94J ARG* 3.5 47.6 - - + +
95J TYR* 3.5 43.5 - - + +
105K LYS* 3.9 14.4 - - - +
220K GLU* 5.1 2.7 - - - +
221K PRO* 5.8 0.9 - - - -
222K LYS* 4.3 10.8 - - - +
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Residues in contact with ARG 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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81J GLU* 2.7 49.9 + - - +
82J HIS* 4.1 1.3 - - - +
84J MET* 1.3 74.4 - - + +
86J ASN* 1.3 73.1 + - - +
44K PHE* 3.0 34.0 + - - +
45K VAL* 4.0 17.6 - - - +
46K PRO* 4.2 12.0 - - + +
49K SER* 5.5 1.6 + - - -
52K GLU* 4.6 3.3 - - - +
101K SER 3.8 9.5 + - - -
102K LEU* 4.1 2.4 - - - +
217K TRP* 6.3 0.2 - - - -
218K ALA 2.8 30.1 + - - -
219K ALA* 3.7 13.7 + - - +
221K PRO* 3.5 25.2 - - + +
222K LYS* 3.2 31.1 + - - +
42L ALA* 4.8 1.7 - - - +
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Residues in contact with ASN 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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82J HIS* 2.6 53.7 + - + +
84J MET 3.6 0.6 - - - -
85J ARG* 1.3 89.0 - - - +
87J VAL* 1.3 70.4 + - - +
88J ASN* 3.3 4.2 + - - +
46K PRO* 4.6 6.0 - - - +
48K ARG* 3.0 32.7 + - - +
52K GLU* 5.4 0.2 - - - +
88K HIS* 5.5 6.3 - - - -
222K LYS* 5.8 1.0 - - - -
41L SER* 4.0 1.5 - - - -
42L ALA* 3.5 26.5 + - - +
43L ASP* 3.9 13.9 - - - +
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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