Contacts of the helix formed by residues 69 - 86 (chain X) in PDB entry 3CR4
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 69 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14X PHE* 3.7 3.6 - - - -
25X HIS 4.1 4.5 - - - +
26X LYS* 3.9 30.0 + - + +
63X ASP* 4.1 14.3 - - - +
65X ASP* 5.7 1.5 - - - +
67X GLU 3.9 1.0 + - - -
68X CYS* 1.3 74.8 - - - +
70X PHE* 1.3 60.5 + - - +
71X GLN* 3.4 11.7 + - - +
72X GLU* 2.8 42.9 + - - +
73X PHE* 2.8 27.5 + - - +
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Residues in contact with PHE 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LEU* 4.6 0.9 - - + -
11X ILE* 4.0 43.7 - - + -
14X PHE* 3.6 43.3 - + + -
15X HIS* 4.8 4.0 - + + -
25X HIS 4.3 2.0 + - - +
69X ASP* 1.3 76.7 - - - +
71X GLN* 1.3 61.3 + - + +
73X PHE* 3.1 10.5 + + - +
74X MET* 2.9 53.7 + - + +
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Residues in contact with GLN 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X ASP* 3.4 13.3 + - - +
70X PHE* 1.3 82.4 - - + +
72X GLU* 1.3 64.4 + - + +
74X MET* 3.2 11.2 + - - +
75X ALA* 3.1 25.3 + - - +
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Residues in contact with GLU 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LEU* 3.3 28.0 - - - +
61X ASP* 4.0 0.2 - - - -
62X SER* 2.9 27.9 + - - +
63X ASP* 3.1 12.3 + - - +
67X GLU 3.0 4.5 - - - +
68X CYS* 3.3 10.6 - - - -
69X ASP* 2.8 39.2 + - - +
71X GLN* 1.3 79.9 - - + +
73X PHE* 1.3 64.2 + - - +
75X ALA* 3.4 8.3 + - - +
76X PHE* 3.1 20.6 + - - +
104X CA 2.5 30.4 - - - -
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Residues in contact with PHE 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LEU* 3.5 25.6 - - + -
13X VAL* 3.8 20.6 - - + -
14X PHE* 3.5 29.2 - + + -
27X LEU* 3.9 15.3 - - + -
35X LEU* 4.0 24.9 - - + -
68X CYS* 3.4 7.7 - - - -
69X ASP 2.8 14.4 + - - +
70X PHE* 3.1 15.7 + + - +
72X GLU* 1.3 74.8 - - - +
74X MET* 1.3 64.1 + - - +
76X PHE* 3.2 28.4 + + - +
77X VAL* 2.9 47.2 + - + +
80X ILE* 6.2 0.2 - - + -
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Residues in contact with MET 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LEU* 3.9 33.0 - - + -
70X PHE* 2.9 49.4 + - + +
71X GLN* 3.2 13.2 + - - +
73X PHE* 1.3 79.3 - - - +
75X ALA* 1.3 59.9 + - - +
77X VAL* 3.4 10.6 + - + +
78X ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X LEU* 5.9 1.1 - - + +
71X GLN 3.1 12.6 + - - +
72X GLU* 3.7 10.5 - - - +
73X PHE 3.3 0.2 - - - -
74X MET* 1.3 73.2 - - - +
76X PHE* 1.3 59.7 + - - +
78X ALA* 3.1 10.0 + - - +
79X MET* 2.9 42.8 + - + +
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Residues in contact with PHE 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X LEU* 4.2 9.2 - - + -
35X LEU* 4.6 5.8 - - + -
36X ILE* 3.9 29.8 - - + -
40X LEU* 3.9 13.2 - - + -
44X LEU* 4.1 9.2 - - + -
56X VAL* 4.5 10.3 - - + -
60X LEU* 3.6 40.9 - - + +
72X GLU 3.1 13.8 + - - +
73X PHE* 3.2 29.4 - + - +
75X ALA* 1.3 75.0 - - - +
77X VAL* 1.3 61.2 + - - +
79X MET* 3.2 15.0 + - + +
80X ILE* 3.0 55.9 + - + +
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Residues in contact with VAL 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LEU* 4.0 36.8 - - + -
73X PHE* 2.9 51.3 + - + +
74X MET* 3.6 15.7 - - + +
76X PHE* 1.3 71.4 - - - +
78X ALA* 1.3 58.5 + - - +
80X ILE* 3.3 13.5 + - + +
81X THR* 2.8 45.5 + - - +
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Residues in contact with ALA 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X MET 3.0 13.9 + - - +
75X ALA* 3.3 12.6 - - - +
77X VAL* 1.3 77.6 - - - +
79X MET* 1.3 55.3 + - - +
81X THR* 4.1 4.4 - - - -
82X THR* 2.8 39.3 + - - +
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Residues in contact with MET 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X THR* 4.0 25.6 - - + +
60X LEU* 3.8 33.2 - - + -
75X ALA* 2.9 25.7 + - + +
76X PHE* 3.3 15.0 - - + +
78X ALA* 1.3 75.1 - - - +
80X ILE* 1.3 59.8 + - + +
82X THR* 3.5 5.2 + - - -
83X ALA* 3.0 28.8 + - - +
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Residues in contact with ILE 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X LEU* 3.6 36.6 - - + -
43X PHE* 3.9 33.4 - - + -
44X LEU* 4.8 9.4 - - + -
73X PHE* 6.2 0.2 - - + -
76X PHE* 3.0 44.6 + - + +
77X VAL* 3.6 12.8 - - + +
79X MET* 1.3 72.5 - - + +
81X THR* 1.3 62.0 + - - +
83X ALA* 3.2 8.3 + - - +
84X CYS* 2.9 26.6 + - + +
88X PHE* 5.1 2.4 - - + -
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Residues in contact with THR 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X VAL* 2.8 37.0 + - - +
78X ALA* 4.1 4.5 - - - -
80X ILE* 1.3 72.8 - - - +
82X THR* 1.3 56.1 + - - +
84X CYS* 3.2 8.3 + - + +
85X HIS* 2.8 34.4 + - + +
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Residues in contact with THR 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X ALA* 2.8 24.7 + - - +
79X MET* 3.8 6.1 - - - -
81X THR* 1.3 75.6 - - - +
83X ALA* 1.3 57.3 + - - +
85X HIS* 3.3 11.8 + - + +
86X GLU* 3.0 48.7 + - + +
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Residues in contact with ALA 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X MET 3.0 18.8 + - - +
80X ILE* 3.5 6.7 - - - +
82X THR* 1.3 74.1 - - - +
84X CYS* 1.3 59.4 + - - +
86X GLU* 3.2 14.5 + - - +
88X PHE* 2.7 49.9 + - + +
89X GLU* 5.8 2.0 - - - +
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Residues in contact with CYS 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X PHE* 4.2 24.0 - - + -
80X ILE 2.9 13.5 + - - +
81X THR* 3.5 12.3 - - + +
83X ALA* 1.3 73.9 - - - +
85X HIS* 1.3 54.2 - - - +
87X PHE* 2.8 14.7 + - - -
88X PHE* 3.8 22.9 - - + -
101X PNT 2.8 60.3 - - - +
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Residues in contact with HIS 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X THR* 2.8 21.0 + - + +
82X THR* 3.4 13.0 + - - +
84X CYS* 1.3 75.5 - - - +
86X GLU* 1.3 63.8 + - + +
87X PHE* 3.3 9.4 + - - -
101X PNT 3.1 55.4 + - - -
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Residues in contact with GLU 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X THR* 3.0 36.6 + - + +
83X ALA* 3.2 8.5 + - - +
84X CYS 3.1 0.4 - - - -
85X HIS* 1.3 84.1 - - + +
87X PHE* 1.3 73.1 + - - +
88X PHE 3.2 1.0 + - - -
89X GLU* 3.4 22.0 + - - +
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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