Contacts of the helix formed by residues 71 - 87 (chain A) in PDB entry 4X4R
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 SER 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU 3.4 3.4 + - - -
70A PHE* 1.3 76.4 - - - +
72A LYS* 1.3 62.2 + - - +
73A GLU* 3.1 24.2 + - - -
74A GLU* 3.1 26.6 + - - -
75A LEU* 2.9 24.1 + - - +
115A TYR* 3.5 2.6 + - - -
124A LYS* 5.2 1.3 - - - +
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Residues in contact with LYS 72 (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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71A SER* 1.3 72.3 - - - +
73A GLU* 1.3 68.8 + - - +
75A LEU* 3.8 10.9 - - - +
76A ARG* 3.2 22.3 + - - +
96A GLU* 3.5 23.6 + - - +
97A HIS* 4.0 10.7 + - - -
98A PRO* 4.9 7.5 - - - +
115A TYR* 3.6 14.7 + - + +
124A LYS* 4.7 10.4 + - - +
125A SER* 3.6 28.2 + - - +
126A ALA 5.3 0.4 - - - +
31B C 4.2 22.9 - - - +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.1 21.6 + - - -
72A LYS* 1.3 83.8 + - + +
74A GLU* 1.3 60.5 + - + +
76A ARG* 3.3 23.9 + - - +
77A GLU* 2.9 41.5 + - - +
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Residues in contact with GLU 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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69A GLU 4.6 1.2 - - - +
70A PHE* 3.5 30.8 - - + -
71A SER* 3.1 36.7 + - - +
73A GLU* 1.3 77.2 - - + +
75A LEU* 1.3 64.4 + - - +
77A GLU* 4.2 8.9 - - - +
78A ARG* 3.1 32.0 + - + +
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Residues in contact with LEU 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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66A PHE* 3.7 27.0 - - + -
70A PHE* 4.4 6.6 - - + -
71A SER 2.9 15.9 + - - +
72A LYS* 3.8 11.9 - - - +
73A GLU 3.3 0.2 - - - -
74A GLU* 1.3 78.3 - - - +
76A ARG* 1.3 57.4 + - - +
78A ARG* 4.3 1.1 - - - +
79A GLY* 3.0 27.0 + - - -
97A HIS* 4.2 14.1 - - + -
98A PRO* 5.6 3.6 - - + -
113A PRO* 3.8 9.7 - - + +
114A CYS* 3.7 31.4 - - - +
115A TYR* 3.7 25.8 - - + +
125A SER* 3.5 24.9 - - - +
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Residues in contact with ARG 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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72A LYS 3.2 11.1 + - - +
73A GLU* 3.5 23.6 + - - +
74A GLU 3.3 0.2 - - - -
75A LEU* 1.3 77.5 - - - +
77A GLU* 1.3 98.1 + - - +
79A GLY 3.3 0.5 + - - -
80A LEU* 3.0 45.2 + - + +
94A TYR* 3.6 21.5 - - - -
98A PRO* 3.9 31.1 - - + +
113A PRO* 5.3 0.6 - - - +
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Residues in contact with GLU 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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73A GLU* 2.9 27.9 + - - +
74A GLU* 4.2 9.3 - - - +
76A ARG* 1.3 107.8 + - - +
78A ARG* 1.3 59.7 + - + +
80A LEU* 4.6 3.5 - - - +
81A GLU* 3.3 26.7 + - - +
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Residues in contact with ARG 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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38A LEU 5.8 0.2 + - - -
40A VAL* 4.1 11.5 - - - +
66A PHE* 3.9 25.8 - - + -
70A PHE* 4.3 16.0 - - + -
74A GLU* 3.1 20.3 + - + +
75A LEU 4.3 1.1 - - - +
77A GLU* 1.3 79.4 - - + +
79A GLY* 1.3 64.5 + - - +
81A GLU* 3.2 36.7 + - - +
82A ILE* 3.1 59.7 + - - +
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Residues in contact with GLY 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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64A LEU* 4.2 6.5 - - - +
66A PHE* 4.1 9.5 - - - -
75A LEU 3.0 20.4 + - - -
78A ARG* 1.3 77.9 - - - +
80A LEU* 1.3 56.9 + - - +
82A ILE* 3.4 2.6 + - - +
83A GLY* 3.0 24.9 + - - -
100A VAL* 4.4 2.6 - - - +
111A VAL* 4.9 1.7 - - - +
113A PRO* 3.5 26.3 - - - +
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Residues in contact with LEU 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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76A ARG* 3.0 43.5 + - + +
77A GLU* 4.6 3.4 - - - +
79A GLY* 1.3 72.9 - - - +
81A GLU* 1.3 60.2 + - - +
84A LYS* 2.9 51.7 + - - +
92A ILE* 4.0 26.9 - - + -
94A TYR* 5.1 4.3 - - + +
98A PRO* 4.6 5.2 - - + -
99A TYR* 3.7 24.5 - - - +
100A VAL* 3.4 25.6 - - + -
113A PRO* 5.6 0.7 - - + -
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Residues in contact with GLU 81 (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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77A GLU 3.3 19.1 + - - +
78A ARG* 3.2 42.7 + - - +
80A LEU* 1.3 81.5 - - - +
82A ILE* 1.3 63.2 + - + +
84A LYS* 4.2 11.4 - - - +
85A ALA* 3.4 19.6 + - - +
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Residues in contact with ILE 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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35A LEU* 4.4 3.8 - - + -
38A LEU* 4.0 28.5 - - + +
40A VAL* 3.6 29.2 - - + -
64A LEU* 3.4 30.1 - - + -
66A PHE* 4.4 4.7 - - + -
78A ARG* 3.1 49.3 + - - +
81A GLU* 1.3 75.3 - - + +
83A GLY* 1.3 67.2 + - - +
85A ALA* 3.1 13.2 + - + +
86A VAL* 3.2 21.4 + - + +
111A VAL* 5.1 0.4 - - + -
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Residues in contact with GLY 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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79A GLY 3.0 15.0 + - - -
80A LEU 3.3 3.1 + - - -
82A ILE* 1.3 76.6 - - - +
84A LYS* 1.3 61.9 + - - +
86A VAL* 3.1 11.7 + - - +
87A LEU* 3.2 22.1 + - - +
100A VAL* 4.0 14.1 - - - -
111A VAL* 3.9 24.6 - - - +
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Residues in contact with LYS 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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80A LEU* 2.9 40.5 + - - +
81A GLU* 4.2 8.4 - - - +
83A GLY* 1.3 74.5 - - - +
85A ALA* 1.3 60.9 + - - +
86A VAL 3.4 0.5 + - - -
87A LEU 3.6 15.0 - - - +
90A TYR* 3.4 63.8 + - + +
92A ILE* 4.2 13.2 - - + +
100A VAL* 4.5 3.1 - - + +
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Residues in contact with ALA 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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34A ARG* 5.1 5.0 - - - +
38A LEU* 4.0 23.2 - - + +
81A GLU 3.4 12.2 + - - +
82A ILE* 3.1 11.5 + - - +
84A LYS* 1.3 79.1 - - - +
86A VAL* 1.3 60.4 + - - +
87A LEU 3.7 1.4 - - - +
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Residues in contact with VAL 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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31A LEU* 3.3 29.8 - - + -
34A ARG* 2.7 52.7 + - + +
35A LEU* 3.7 32.1 - - + -
38A LEU* 3.8 16.2 - - + -
82A ILE* 3.3 17.5 - - + +
83A GLY* 3.1 6.0 + - - +
85A ALA* 1.3 82.7 - - - +
87A LEU* 1.3 58.1 + - + +
104A VAL* 3.8 2.8 - - - +
111A VAL* 5.3 4.7 - - + -
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Residues in contact with LEU 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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31A LEU* 4.5 3.1 - - + -
34A ARG* 4.1 0.9 - - - -
83A GLY 3.2 12.4 + - - +
84A LYS 3.6 12.9 - - - +
85A ALA 3.7 0.9 - - - +
86A VAL* 1.3 80.3 - - + +
88A ASP* 1.3 66.3 + - - +
89A SER 4.0 8.6 - - - +
90A TYR* 4.1 8.8 - - + -
100A VAL* 3.5 33.4 - - + +
102A GLY* 3.7 21.5 - - - +
103A VAL 3.8 6.3 - - - +
104A VAL* 3.4 22.7 - - + -
109A VAL* 3.6 26.9 - - + +
111A VAL* 3.8 16.4 - - + -
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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