Contacts of the helix formed by residues 63 - 85 (chain U) in PDB entry 6CP3
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 GLY 63 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61U ALA 4.1 0.6 + - - -
62U SER* 1.3 72.2 - - - +
64U LYS* 1.3 56.9 + - - +
65U PRO* 3.4 2.0 - - - -
66U LEU* 2.9 40.0 + - - +
67U TRP* 3.2 4.1 + - - +
58X TRP* 3.9 14.4 - - - -
74Z ALA* 6.1 3.6 - - - +
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Residues in contact with LYS 64 (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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55U TYR* 4.6 21.9 - - - -
60U ASN* 5.6 6.1 - - - +
62U SER* 3.1 29.1 + - - -
63U GLY* 1.3 74.6 - - - +
65U PRO* 1.4 53.7 - - + +
67U TRP* 2.8 18.2 - - + +
68U HIS* 2.5 48.8 + - + +
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Residues in contact with PRO 65 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U TYR* 3.7 13.8 + - - +
55U TYR* 3.5 39.5 - - + +
56U PHE* 3.6 28.7 - - + -
62U SER 3.2 14.4 - - - +
63U GLY 3.6 2.2 - - - -
64U LYS* 1.4 88.8 - - + +
66U LEU* 1.3 52.7 + - - +
68U HIS* 3.0 13.3 + - + +
69U PHE* 2.4 38.8 + - - +
58X TRP* 4.5 2.2 - - + -
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Residues in contact with LEU 66 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U GLY* 2.9 19.2 + - - +
65U PRO* 1.3 76.5 - - - +
67U TRP* 1.3 48.7 + - - +
69U PHE* 3.0 12.3 + - + +
70U ALA* 2.4 39.1 + - - +
58X TRP* 3.6 36.1 - - + -
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Residues in contact with TRP 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U GLY 3.2 3.1 + - - +
64U LYS* 2.8 25.3 + - + +
66U LEU* 1.3 76.7 - - - +
68U HIS* 1.3 69.8 + + - -
70U ALA* 3.0 12.9 + - + +
71U LEU* 2.8 41.5 + - + +
62Z PHE* 5.5 2.5 - + - -
63Z LEU* 4.1 21.8 - - + -
66Z THR* 3.3 43.7 - - + -
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Residues in contact with HIS 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U TYR* 4.5 9.4 - + + +
55U TYR* 3.2 32.2 + + - -
64U LYS* 2.5 41.9 + - + +
65U PRO* 3.2 13.2 - - + +
67U TRP* 1.3 79.8 - + - +
69U PHE* 1.3 52.4 + - - +
71U LEU* 3.0 16.0 + - - +
72U GLY* 2.7 31.7 + - - -
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Residues in contact with PHE 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51U TYR* 5.4 1.3 + - - +
65U PRO 2.4 29.9 + - - +
66U LEU* 3.4 14.8 - - + +
68U HIS* 1.3 64.8 - - - +
70U ALA* 1.3 66.6 + - - +
72U GLY* 3.0 13.8 + - - +
73U ILE* 3.1 39.2 + - + +
35X ILE* 4.3 15.7 - - + -
38X LEU* 6.5 1.1 - - + -
39X VAL* 3.6 33.9 - - + -
102X ILE* 6.1 2.5 - - + -
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Residues in contact with ALA 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U LEU 2.4 26.2 + - - +
67U TRP* 3.2 18.4 - - + +
69U PHE* 1.3 70.7 - - - +
71U LEU* 1.3 61.9 + - - +
73U ILE* 3.0 10.6 + - - +
74U ILE* 3.0 25.5 + - + +
105X ILE* 4.6 13.6 - - + +
62Z PHE* 4.5 24.0 - - + -
66Z THR* 6.1 0.4 - - + -
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Residues in contact with LEU 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U TRP* 2.8 25.4 + - + +
68U HIS* 3.4 16.8 - - - +
70U ALA* 1.3 74.0 - - - +
72U GLY* 1.3 51.9 + - - +
74U ILE* 3.0 33.4 + - + +
75U ALA* 2.5 37.4 + - + +
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Residues in contact with GLY 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68U HIS 2.7 14.7 + - - -
69U PHE* 3.0 10.8 + - - -
71U LEU* 1.3 76.3 - - - +
73U ILE* 1.3 57.2 + - - +
75U ALA* 3.0 11.2 + - - +
76U PHE* 2.8 28.1 + - - +
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Residues in contact with ILE 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 3.1 43.0 + - + +
70U ALA* 3.0 7.6 + - - +
72U GLY* 1.3 73.5 - - - +
74U ILE* 1.3 61.6 + - - +
76U PHE* 3.0 24.7 + - + +
77U GLY 3.3 11.5 + - - +
78U TYR 4.7 0.5 + - - -
35X ILE* 5.6 9.4 - - + -
101X LEU 5.7 0.7 - - - +
102X ILE* 4.7 23.3 - - + +
105X ILE* 3.7 40.8 - - + -
107X TYR* 4.1 14.8 - - - +
108X SER* 5.1 4.0 - - - -
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Residues in contact with ILE 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70U ALA* 3.0 16.1 + - + +
71U LEU* 3.0 35.9 + - + +
73U ILE* 1.3 77.1 - - - +
75U ALA* 1.3 58.0 + - - +
76U PHE 3.5 0.2 + - - -
78U TYR* 3.5 24.9 - - + +
105X ILE* 4.3 12.6 - - + -
106X PRO* 5.8 0.2 - - + -
107X TYR* 5.5 6.9 - - + -
59Z LEU* 3.8 40.8 - - + -
62Z PHE* 4.8 17.5 - - + -
63Z LEU* 5.5 6.3 - - + -
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Residues in contact with ALA 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71U LEU* 2.5 18.3 + - + +
72U GLY* 3.0 14.8 + - - +
74U ILE* 1.3 75.6 - - - +
76U PHE* 1.3 60.8 + - - +
78U TYR* 4.7 0.7 - - - -
79U SER* 3.6 15.2 + - - -
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Residues in contact with PHE 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72U GLY 2.8 13.7 + - - +
73U ILE* 3.0 17.0 + - + +
75U ALA* 1.3 77.2 - - - +
77U GLY* 1.3 66.8 + - - +
79U SER* 2.5 27.7 + - - -
80U MET* 3.3 37.9 + - + +
28X THR* 6.3 0.4 - - - -
31X LEU* 3.5 39.5 - - + -
32X TYR* 4.8 15.0 - + - -
35X ILE* 5.0 8.5 - - + -
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Residues in contact with GLY 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73U ILE* 3.3 8.1 + - - +
76U PHE* 1.3 87.7 - - - +
78U TYR* 1.3 54.0 + - - +
80U MET* 2.9 12.6 + - - +
81U GLU* 2.6 32.6 + - - +
107X TYR* 4.3 19.5 + - - -
108X SER* 5.8 1.3 - - - -
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Residues in contact with TYR 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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74U ILE* 3.5 22.0 + - + +
75U ALA 5.1 0.7 - - - +
76U PHE 3.3 0.8 - - - -
77U GLY* 1.3 74.0 - - - +
79U SER* 1.3 62.2 + - - +
81U GLU* 2.7 38.9 + - + +
82U TYR* 3.0 42.8 + + - +
107X TYR* 4.1 44.1 - + + +
53Z ASN* 4.9 10.1 + - - -
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Residues in contact with SER 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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75U ALA 3.6 12.3 + - - -
76U PHE* 2.5 26.5 + - - -
78U TYR* 1.3 79.3 - - - +
80U MET* 1.3 57.2 + - - +
82U TYR* 2.9 17.1 + - - +
83U TYR* 2.9 22.7 + - - +
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Residues in contact with MET 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 PHE* 3.3 36.7 + - + +
77U GLY* 2.9 18.4 + - - +
79U SER* 1.3 77.5 + - - +
81U GLU* 1.3 54.2 - - - +
83U TYR* 2.9 12.6 + - + +
84U PHE* 2.6 60.7 + - + +
28X THR* 3.7 33.2 - - + -
31X LEU* 4.9 5.6 - - + -
32X TYR* 5.7 4.3 - - - -
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Residues in contact with GLU 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 GLY 2.6 13.3 + - - +
78U TYR* 2.7 37.0 - - + +
80U MET* 1.3 71.4 - - - +
82U TYR* 1.3 63.5 + - + +
84U PHE* 3.0 4.5 + - - +
85U HIS* 2.6 82.0 + - - +
107X TYR* 5.1 9.5 - - + -
53Z ASN* 5.4 7.8 + - - +
55Z GLU* 4.9 7.7 - - - +
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Residues in contact with TYR 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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78U TYR* 3.0 47.3 + + - -
79U SER* 2.9 16.7 + - - +
81U GLU* 1.3 82.7 - - + +
83U TYR* 1.3 58.1 + - - +
84U PHE 5.1 0.2 - - - -
85U HIS 5.1 4.7 - - - -
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Residues in contact with TYR 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79U SER 2.9 10.4 + - - +
80U MET* 2.9 15.7 + - + +
82U TYR* 1.3 78.8 - - - +
84U PHE* 1.3 88.4 + + - +
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Residues in contact with PHE 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 MET* 2.6 44.5 + - + +
81U GLU* 3.0 2.4 + - - -
83U TYR* 1.3 109.4 - + - +
85U HIS* 1.3 64.9 + - + +
28X THR* 4.5 13.5 - - + -
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Residues in contact with HIS 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81U GLU* 2.6 61.4 + - - +
82U TYR* 5.1 5.3 - - - -
84U PHE* 1.3 80.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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