Contacts of the helix formed by residues 76 - 93 (chain A) in PDB entry 4R8U
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 ARG 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.7 2.0 - - - +
18A GLU* 3.0 39.3 + - - +
21A ASP* 3.0 35.1 + - - +
74A PRO* 5.8 3.1 - - + -
75A GLY* 1.3 78.9 - - - +
77A PHE* 1.3 66.3 + - - +
78A ASP* 3.3 2.9 - - + -
79A ALA* 3.0 33.1 + - + +
80A TYR* 3.2 23.6 + - - -
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Residues in contact with PHE 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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14A PHE* 6.3 0.9 - + - -
75A GLY 4.0 1.8 + - - -
76A ARG* 1.3 73.0 - - - +
78A ASP* 1.3 67.8 + - - +
80A TYR* 3.0 13.5 + + + +
81A LYS* 2.7 67.1 + - + +
103A LEU* 4.1 29.2 - - + -
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.3 1.2 - - + -
77A PHE* 1.3 92.5 - - - +
79A ALA* 1.3 62.8 + - - +
81A LYS* 3.7 5.7 - - - +
82A GLU* 3.0 26.3 + - - +
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Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 18.3 - - + +
20A ARG* 5.0 3.5 + - - +
21A ASP* 4.6 1.1 - - - +
76A ARG* 3.0 46.9 + - + +
78A ASP* 1.3 79.1 - - - +
80A TYR* 1.3 63.4 + - + +
82A GLU* 3.4 6.0 + - - +
83A ALA* 3.2 21.8 + - - +
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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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13A PHE* 3.6 24.5 - - + -
14A PHE* 3.6 57.7 - + + -
17A VAL* 4.0 22.2 - - + -
18A GLU* 2.7 29.7 + - - +
32A ILE* 3.8 10.4 - - + +
75A GLY* 3.2 17.9 - - - -
76A ARG 3.4 27.8 - - - -
77A PHE* 3.0 11.1 + + - +
79A ALA* 1.3 76.2 - - + +
81A LYS* 1.3 61.4 + - - +
83A ALA* 3.4 1.6 + - - -
84A SER* 3.0 28.5 + - - -
103A LEU* 4.0 11.4 - - + -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 2.7 49.9 + - + +
78A ASP* 3.7 8.1 - - - +
80A TYR* 1.3 74.5 - - - +
82A GLU* 1.3 57.7 + - - +
84A SER* 3.2 4.2 + - - -
85A ASN* 2.9 52.9 + - - +
88A ARG* 4.4 14.8 - - - +
103A LEU* 4.1 23.1 - - + +
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Residues in contact with GLU 82 (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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78A ASP 3.0 17.4 + - - +
79A ALA* 3.9 6.0 - - - +
81A LYS* 1.3 76.9 - - - +
83A ALA* 1.3 64.0 + - - +
85A ASN* 3.5 10.2 + - + +
86A HIS* 3.2 24.2 + - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.9 20.9 - - + -
17A VAL* 4.5 4.0 - - + -
20A ARG* 5.0 6.1 - - - +
79A ALA 3.2 13.4 + - - +
80A TYR* 3.6 9.2 - - - +
81A LYS 3.2 0.2 - - - -
82A GLU* 1.3 77.7 - - - +
84A SER* 1.3 56.5 + - - +
86A HIS* 3.5 0.7 + - - -
87A ILE* 3.0 36.0 + - + +
135A LEU* 3.5 21.9 - - + +
137A LEU* 4.2 9.4 - - + -
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.5 1.5 - - - -
80A TYR 3.0 18.0 + - - -
81A LYS* 3.2 6.9 + - - +
83A ALA* 1.3 75.4 - - - +
85A ASN* 1.3 67.4 + - - +
87A ILE* 3.4 7.9 + - - +
88A ARG* 2.9 42.0 + - - +
103A LEU* 2.9 48.6 + - - +
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Residues in contact with ASN 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 LYS* 2.9 50.2 + - - +
82A GLU* 3.8 8.7 - - + +
83A ALA 3.4 0.2 - - - -
84A SER* 1.3 76.0 + - - +
86A HIS* 1.3 58.1 + - - +
88A ARG* 3.2 12.3 + - - +
89A GLU* 2.9 30.9 + - - +
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Residues in contact with HIS 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 GLU* 3.2 17.7 + - + +
83A ALA* 3.7 4.0 - - - +
85A ASN* 1.3 77.6 - - - +
87A ILE* 1.3 57.8 + - - +
89A GLU* 3.2 14.6 + - - +
90A ILE* 2.9 39.0 + - + +
93A ARG* 4.3 1.2 + - - -
134A GLU* 2.8 48.1 + - + +
135A LEU* 3.9 16.7 - - + +
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Residues in contact with ILE 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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10A MET* 3.4 41.5 - - + -
13A PHE* 4.7 6.7 - - + -
83A ALA 3.0 26.9 + - - +
84A SER* 3.6 8.1 - - - +
86A HIS* 1.3 75.3 - - - +
88A ARG* 1.3 59.0 + - + +
90A ILE* 3.0 11.9 + - - +
91A PHE* 2.9 58.0 + - + -
103A LEU 5.4 5.6 - - - +
104A ASP 5.7 2.0 - - - +
131A ILE* 4.1 20.4 - - + -
135A LEU* 4.0 15.5 - - + -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 4.4 14.9 - - - +
84A SER* 2.9 38.0 + - - +
85A ASN* 3.2 11.3 + - - +
87A ILE* 1.3 74.3 - - + +
89A GLU* 1.3 61.4 + - - +
91A PHE* 3.2 24.2 + - + +
92A SER* 3.2 21.0 + - - -
98A ILE* 4.2 8.3 - - + +
100A PRO* 3.6 35.0 - - + +
102A SER* 2.8 36.0 + - - +
103A LEU* 3.8 7.6 + - - +
105A GLU 5.4 0.8 + - - -
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Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN 2.9 13.8 + - - +
86A HIS* 3.5 18.4 + - - +
88A ARG* 1.3 75.7 - - - +
90A ILE* 1.3 61.6 + - - +
92A SER* 2.5 29.8 + - - +
93A ARG* 2.9 47.3 + - - +
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Residues in contact with ILE 90 (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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86A HIS* 2.9 32.4 + - + +
87A ILE* 3.2 8.3 - - - +
89A GLU* 1.3 74.8 - - - +
91A PHE* 1.3 66.5 + - - +
93A ARG* 3.1 49.2 + - - +
94A TYR* 3.5 11.9 - - + -
127A ILE* 4.7 11.0 - - + -
130A THR* 4.0 23.6 - - + -
131A ILE* 4.0 26.2 - - + -
134A GLU* 3.8 8.1 - - - +
135A LEU* 3.7 20.0 - - + -
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Residues in contact with PHE 91 (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* 3.8 31.9 - - + -
10A MET* 6.1 0.2 - - - -
87A ILE* 2.9 44.5 + - + -
88A ARG* 3.2 19.0 + - + +
90A ILE* 1.3 75.2 - - + +
92A SER* 1.3 58.0 + - - +
94A TYR* 2.9 25.4 + - - +
95A THR* 3.3 12.1 + - - +
98A ILE* 3.6 19.4 - - + +
104A ASP 5.7 0.9 - - - -
105A GLU* 5.0 4.3 - - - -
106A ALA* 3.8 25.6 - - + -
108A LEU* 3.9 28.6 - - + +
127A ILE* 3.8 28.9 - - + -
131A ILE* 4.1 2.5 - - + -
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Residues in contact with SER 92 (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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88A ARG 3.2 9.6 + - - -
89A GLU* 2.5 29.8 + - - +
91A PHE* 1.3 78.9 - - - +
93A ARG* 1.3 61.1 + - - +
94A TYR 3.1 1.5 + - - -
95A THR 3.3 19.4 + - - +
96A SER* 5.8 0.9 - - - -
98A ILE* 3.7 7.9 - - - -
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 4.3 1.2 + - - -
89A GLU* 2.9 43.9 + - - +
90A ILE* 3.1 26.0 + - - +
92A SER* 1.3 79.5 + - - +
94A TYR* 1.3 69.8 + - + +
115A HIS* 3.4 18.0 + - - -
130A THR* 3.6 12.3 - - - +
134A GLU* 2.7 44.3 + - - -
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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
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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