Contacts of the helix formed by residues 73 - 88 (chain A) in PDB entry 4R54
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ALA* 1.3 80.1 - - - +
74A SER* 1.3 66.3 + - - -
75A SER* 3.3 3.1 - - - -
76A THR 3.2 4.5 + - - -
77A SER* 3.1 17.8 + - - -
95A THR* 3.5 9.9 - - - +
403A NAP 3.6 25.6 + - - -
405A 3JM 3.2 12.1 - - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY* 1.3 71.1 - - - -
75A SER* 1.3 51.8 + - - -
77A SER* 3.2 2.4 + - - -
78A ALA* 2.8 36.4 + - - +
95A THR* 3.7 16.3 - - - +
96A SER* 3.1 24.4 + - - -
97A TYR* 3.7 19.9 + - - +
405A 3JM 2.6 29.3 + - - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 3.3 1.1 - - - -
74A SER* 1.3 79.0 - - - +
76A THR* 1.3 57.4 + - - +
78A ALA* 3.2 7.4 + - - +
79A LYS* 2.9 55.8 + - - +
405A 3JM 4.1 3.2 + - - -
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Residues in contact with THR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.1 13.5 - - + -
57A THR* 4.5 0.4 - - + -
70A PHE* 4.0 2.8 - - + -
72A ALA* 3.2 41.8 + - + -
73A GLY 3.2 3.8 + - - -
75A SER* 1.3 78.1 + - - +
77A SER* 1.3 58.1 + - - +
79A LYS* 4.5 4.2 - - - +
80A TYR* 3.0 50.1 + - + +
403A NAP 3.3 35.7 + - + -
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.5 21.4 - - - +
72A ALA 5.4 0.7 + - - -
73A GLY 3.1 7.2 + - - -
74A SER 3.2 6.5 + - - -
76A THR* 1.3 76.3 - - - +
78A ALA* 1.3 64.8 + - - +
81A ALA* 2.9 28.0 + - - +
82A PRO* 3.5 1.9 - - - +
93A ASP* 2.5 42.0 + - - -
95A THR* 3.4 14.7 - - - +
97A TYR* 4.7 0.2 - - - -
98A PHE* 3.5 7.9 - - - -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A SER 2.8 20.6 + - - +
75A SER* 3.5 9.2 - - - +
77A SER* 1.3 74.4 - - - +
79A LYS* 1.3 62.1 + - + +
82A PRO* 3.5 15.8 - - - +
97A TYR* 3.5 43.9 - - + +
98A PHE* 4.2 2.3 - - - -
358A LYS* 3.8 19.8 + - + +
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A SER* 2.9 41.0 + - - +
76A THR* 4.0 6.0 + - - +
78A ALA* 1.3 82.1 - - + +
80A TYR* 1.3 88.1 + - + +
82A PRO* 4.2 0.9 - - - +
83A TYR* 3.1 28.2 - - - -
358A LYS* 4.6 18.3 + - + +
403A NAP 4.8 12.3 + - - -
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 3.6 39.8 + - + -
58A THR* 3.6 30.0 - - - +
59A GLU* 3.6 24.2 + - + -
62A PHE* 4.2 6.2 - - + -
70A PHE* 4.0 13.5 - - + -
76A THR* 3.0 31.2 + - + +
79A LYS* 1.3 111.2 + - + +
81A ALA* 1.3 67.0 + - - +
82A PRO* 3.2 3.1 - - - -
83A TYR* 3.1 8.1 + - - +
84A ALA* 3.0 19.8 + - - +
403A NAP 4.8 7.5 + - - -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.7 23.5 - - + -
77A SER* 2.9 20.5 + - - +
80A TYR* 1.3 76.8 - - - +
82A PRO* 1.4 59.4 - - + +
84A ALA* 3.1 4.8 + - - +
85A VAL* 2.9 32.1 + - - +
91A VAL* 4.0 19.7 - - + +
93A ASP* 5.6 0.2 - - - -
98A PHE* 3.9 15.5 - - + -
122A ILE* 4.3 4.9 - - + -
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER 3.5 11.7 - - - +
78A ALA 3.5 14.8 - - - +
79A LYS 4.2 2.2 - - - +
80A TYR 3.4 4.9 - - - +
81A ALA* 1.4 91.6 - - + +
83A TYR* 1.3 56.1 + - + +
85A VAL* 3.4 10.1 + - + +
86A LYS* 2.8 29.8 + - - +
98A PHE* 4.2 9.4 - - + -
122A ILE* 5.2 0.2 - - + -
353A LEU* 4.0 2.6 - - + +
355A PHE* 3.8 24.2 - - + +
356A GLU 3.4 26.2 - - - +
357A LEU* 3.8 17.4 - - + +
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU* 3.8 55.0 + - + +
62A PHE* 4.8 2.5 - - + -
79A LYS 3.1 29.2 - - - -
80A TYR* 3.1 8.8 + - - +
82A PRO* 1.3 74.4 - - + +
84A ALA* 1.3 61.8 + - - +
86A LYS* 3.3 11.1 + - + +
87A ALA* 2.9 29.5 + - - +
357A LEU* 3.6 36.0 - - + +
358A LYS 3.0 31.4 + - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.7 38.0 - - + -
70A PHE* 4.5 1.3 - - + -
80A TYR 3.0 11.5 + - - +
81A ALA* 3.1 10.1 + - - +
83A TYR* 1.3 75.2 - - - +
85A VAL* 1.3 61.6 + - - +
87A ALA* 3.2 2.3 + - - +
88A GLY 3.1 5.9 + - - -
89A VAL* 2.9 36.8 + - + +
91A VAL* 3.8 17.5 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ALA 2.9 19.1 + - - +
82A PRO* 3.6 9.0 - - + +
84A ALA* 1.3 76.2 - - - +
86A LYS* 1.3 59.1 + - - +
88A GLY* 2.9 20.3 + - - -
89A VAL 3.9 8.4 - - - +
91A VAL* 4.1 4.3 - - + -
120A ASN 3.8 19.3 - - - +
121A GLY* 3.7 16.8 - - - +
122A ILE* 3.5 32.3 - - + -
350A THR* 4.6 17.1 + - - +
353A LEU* 4.1 19.5 - - + -
355A PHE* 4.4 4.7 - - + -
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO 2.8 21.4 + - - +
83A TYR* 3.3 13.4 + - + +
85A VAL* 1.3 73.9 - - - +
87A ALA* 1.3 62.5 + - - +
88A GLY* 3.3 1.2 + - - -
353A LEU* 4.3 22.9 - - + +
357A LEU* 4.1 29.4 - - + -
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU 6.1 0.9 - - - +
62A PHE* 4.3 20.9 - - + +
63A GLU* 3.7 32.2 - - - +
64A GLY 5.9 0.9 + - - -
65A VAL 5.7 0.2 - - - +
83A TYR 2.9 18.3 + - - +
84A ALA 3.2 6.7 + - - +
86A LYS* 1.3 73.9 - - - +
88A GLY* 1.3 57.4 + - - +
89A VAL* 4.5 1.7 - - + +
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL 4.5 4.9 - - - +
66A ASP* 4.6 2.8 - - - +
85A VAL 2.9 12.7 + - - -
86A LYS 3.2 1.7 - - - -
87A ALA* 1.3 78.4 - - - +
89A VAL* 1.3 65.8 + - - +
90A VAL* 3.9 0.9 + - - +
348A ARG 4.4 0.9 - - - -
349A PRO* 3.4 46.1 - - - +
350A THR 5.0 1.6 - - - -
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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