Contacts of the helix formed by residues 71 - 84 (chain U) in PDB entry 5GJQ
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 71 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56U VAL* 5.0 3.3 - - - +
57U PRO 3.9 13.9 + - - +
69U PHE* 3.9 16.9 - - + -
70U LEU* 1.3 74.1 - - - +
72U HIS* 1.3 61.6 + - - +
73U ASP* 2.8 30.0 + - - +
74U TYR* 3.1 33.0 + - + +
75U LEU* 3.4 22.3 + - - +
101V GLN* 4.0 5.2 + - - +
63W THR* 3.6 10.1 + - - -
64W LEU* 4.5 5.7 - - - +
99W HIS* 5.2 4.9 - - + -
101W GLN* 3.7 22.2 + - - -
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Residues in contact with HIS 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U PHE* 5.3 0.9 - + - -
70U LEU* 2.7 34.8 + - + +
71U ASP* 1.3 71.9 + - - +
73U ASP* 1.3 61.6 + - - +
75U LEU* 3.3 7.7 + - - +
76U GLU* 3.0 36.8 + - - +
111U LEU* 2.5 41.4 - - + +
115U TYR* 3.1 33.7 + - - +
60W VAL* 4.6 28.1 + - + +
63W THR* 4.8 3.4 + - - +
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Residues in contact with ASP 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71U ASP* 2.8 9.7 + - - +
72U HIS* 1.3 76.3 - - - +
74U TYR* 1.3 59.0 + - - +
76U GLU* 3.8 17.5 - - - -
77U ASN* 2.8 49.5 + - - +
62W THR* 5.8 0.4 - - - -
63W THR* 2.7 41.9 + - - +
64W LEU* 3.9 11.9 - - + -
65W THR* 5.1 0.9 - - - -
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Residues in contact with TYR 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U PHE* 4.1 18.4 - + - -
55U ALA 3.2 21.4 + - - -
56U VAL* 4.2 9.2 - - + -
57U PRO* 3.5 16.4 - - + -
71U ASP* 3.1 33.4 + - + +
73U ASP* 1.3 76.8 - - - +
75U LEU* 1.3 57.9 + - - +
77U ASN* 3.8 1.9 - - - +
78U MET* 2.9 46.5 + - + +
98V MET* 2.8 64.3 + - + +
99V LEU* 4.5 1.4 - - - +
101V GLN* 2.4 29.2 - - + +
102V THR* 3.0 15.8 - - - +
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Residues in contact with LEU 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U VAL* 5.1 13.0 - - + -
54U PHE* 5.0 7.2 - - + -
56U VAL* 5.0 16.4 - - + -
70U LEU* 5.4 4.7 - - + -
71U ASP 3.4 14.8 + - - +
72U HIS* 3.3 11.8 + - - +
73U ASP 3.2 0.4 - - - -
74U TYR* 1.3 80.2 - - + +
76U GLU* 1.3 55.9 + - - +
78U MET* 2.7 26.5 + - - -
79U TYR* 2.8 17.8 + - + -
91U ILE* 6.1 3.6 - - + -
115U TYR* 4.4 22.7 - - + -
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Residues in contact with GLU 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72U HIS* 3.0 26.4 + - - +
73U ASP* 3.8 22.7 - - - +
75U LEU* 1.3 75.5 - - - +
77U ASN* 1.3 65.4 + - - +
79U TYR* 4.4 9.4 - - - +
80U GLY* 4.4 9.0 + - - -
115U TYR* 4.6 17.0 + - + -
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Residues in contact with ASN 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73U ASP* 2.8 38.6 + - - +
74U TYR* 3.8 5.3 - - - +
75U LEU 2.8 1.0 + - - -
76U GLU* 1.3 83.7 - - - +
78U MET* 1.3 61.4 + - - +
80U GLY 4.5 0.2 + - - -
81U MET* 3.5 22.1 + - - +
94V LYS* 4.7 23.4 + - - +
98V MET* 4.7 11.0 - - + +
64W LEU* 5.6 4.0 - - - +
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Residues in contact with MET 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U PHE* 3.3 42.0 - - + -
74U TYR* 2.9 40.8 + - + +
75U LEU 2.7 9.3 + - - +
77U ASN* 1.3 70.8 - - - +
79U TYR* 1.3 56.6 + - - +
81U MET* 2.6 49.0 + - + +
82U PHE* 2.9 33.7 + - + -
95V MET* 4.1 16.4 - - - +
98V MET* 4.1 15.5 - - + -
99V LEU* 4.5 10.5 - - + -
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Residues in contact with TYR 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U LEU* 5.7 1.1 - - + -
54U PHE* 4.3 5.7 - - - -
75U LEU 2.8 22.0 + - - +
76U GLU* 4.4 6.1 - - - -
78U MET* 1.3 70.8 - - - +
80U GLY* 1.3 57.1 + - - +
82U PHE* 2.6 31.2 + - - +
83U LYS* 2.8 54.2 + - + -
90U ARG* 3.7 5.9 - - - +
91U ILE* 1.3 109.6 + - + +
115U TYR* 4.2 11.8 + - + -
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Residues in contact with GLY 80 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U GLU 4.4 8.8 + - - -
77U ASN 5.0 0.7 - - - -
78U MET 3.4 0.4 - - - -
79U TYR* 1.3 80.9 - - - +
81U MET* 1.3 56.6 + - - +
82U PHE 3.1 0.2 - - - -
83U LYS* 3.5 16.6 - - - +
84U LYS* 3.2 32.5 + - - +
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Residues in contact with MET 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77U ASN 3.5 13.1 + - - +
78U MET* 2.6 44.8 + - - +
80U GLY* 1.3 73.2 - - - +
82U PHE* 1.3 57.4 + - - -
84U LYS* 4.2 6.3 - - + -
85U VAL* 3.6 0.5 - - - +
91V PHE* 2.7 52.0 - - + +
94V LYS* 3.1 36.1 - - + +
95V MET* 3.2 52.1 - - - +
98V MET* 3.6 14.8 - - + -
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Residues in contact with PHE 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U LEU* 4.1 18.4 - - + -
52U ASN* 3.4 28.5 - - - -
53U SER 4.4 2.2 - - - -
54U PHE* 3.0 51.8 - + + -
78U MET* 2.9 33.8 + - + -
79U TYR 2.6 17.2 + - - +
81U MET* 1.3 71.5 - - - +
83U LYS* 1.3 53.8 + - + +
84U LYS 3.1 1.8 - - - -
85U VAL* 2.7 34.9 + - + +
86U ASN 3.2 15.5 + - - +
89U GLU* 5.4 2.5 - - - +
40V LYS* 5.8 4.3 - - - -
73V PHE* 6.3 1.3 - - + -
74V ALA* 6.2 4.7 - - + -
95V MET* 4.8 14.6 - - + -
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Residues in contact with LYS 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U LEU* 4.6 3.4 - - - +
79U TYR* 2.8 60.5 + - + +
80U GLY* 3.5 15.0 - - - +
82U PHE* 1.3 75.9 - - - +
84U LYS* 1.3 58.0 + - + +
85U VAL 2.9 6.2 + - - -
86U ASN 4.2 1.6 - - - +
87U ALA* 3.4 46.2 + - + +
89U GLU 2.3 34.0 + - - +
90U ARG* 3.3 9.7 - - - +
91U ILE 3.9 0.4 - - - +
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Residues in contact with LYS 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80U GLY 3.2 15.6 + - - +
81U MET* 4.6 3.8 - - + +
82U PHE 3.1 0.4 - - - -
83U LYS* 1.3 76.7 - - - +
85U VAL* 1.3 59.6 + - - +
76V PRO* 2.9 38.2 - - + +
77V GLN 4.4 1.2 + - - -
88V ASP* 5.1 9.1 + - - +
90V VAL* 6.3 2.7 - - - -
91V PHE* 3.8 29.2 - - + +
94V LYS* 6.3 0.9 - - - +
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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