Contacts of the helix formed by residues 69 - 86 (chain A) in PDB entry 3R9X
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 2.8 26.0 + - - -
65A PRO* 3.8 7.8 - - + +
66A LYS* 3.1 24.2 + - + +
67A LYS 3.5 0.4 - - - -
68A SER* 1.3 74.4 + - - +
70A VAL* 1.3 64.8 + - - +
71A LEU* 3.6 11.8 + - - +
72A GLY* 3.0 16.8 + - - -
73A HIS* 2.9 26.7 + - - -
288A ARG* 4.0 11.3 - - - +
289A ARG* 5.2 1.6 - - - -
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Residues in contact with VAL 70 (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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67A LYS 5.9 0.4 - - - +
68A SER* 2.9 15.8 + - - +
69A ASP* 1.3 70.8 - - - +
71A LEU* 1.3 63.4 + - - +
73A HIS* 3.2 9.7 + - + +
74A SER* 2.9 24.2 + - - -
288A ARG 3.3 8.9 + - - +
289A ARG 3.5 26.5 - - - +
291A PRO* 3.9 29.4 - - + -
294A VAL* 3.8 20.0 - - + -
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Residues in contact with LEU 71 (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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39A ARG* 3.6 28.3 - - - +
63A TYR* 5.6 0.7 - - - +
69A ASP* 3.6 8.7 - - - +
70A VAL* 1.3 76.1 - - - +
72A GLY* 1.3 56.3 + - - +
74A SER* 3.3 2.9 + - - -
75A MET* 2.9 44.0 + - + +
287A TRP* 3.9 6.1 - - + -
288A ARG* 3.1 46.5 + - + +
294A VAL* 4.0 13.2 - - + +
299A TYR* 3.9 38.1 - - + +
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Residues in contact with GLY 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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63A TYR* 3.0 31.6 - - - -
65A PRO* 3.7 8.9 - - - +
69A ASP* 3.0 13.3 + - - -
71A LEU* 1.3 78.5 - - - +
73A HIS* 1.3 58.5 + - - +
75A MET* 3.2 5.6 + - - +
76A VAL* 3.0 32.9 + - - +
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Residues in contact with HIS 73 (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 PRO* 4.1 21.5 + - + +
66A LYS 3.1 27.0 + - - -
67A LYS* 3.6 20.7 + - - +
69A ASP 2.9 22.4 + - - +
70A VAL* 3.8 7.4 + - + +
72A GLY* 1.3 73.8 - - - +
74A SER* 1.3 65.1 + - - +
76A VAL* 3.5 6.6 + - + +
77A GLU* 3.1 27.7 + - - +
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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
----------------------------------------------------------
70A VAL* 2.9 18.6 + - - -
71A LEU 3.5 4.7 - - - -
73A HIS* 1.3 77.8 - - - +
75A MET* 1.3 57.1 + - - +
77A GLU* 3.4 8.5 - - - +
78A ILE* 3.0 33.8 + - - +
294A VAL* 4.1 9.8 - - - +
299A TYR 2.5 28.0 + - - -
300A ALA* 3.4 16.6 - - - +
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Residues in contact with MET 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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36A GLY* 4.5 17.5 - - - +
38A THR 3.2 25.1 - - - +
39A ARG* 3.9 26.5 - - + +
60A PRO* 3.7 33.0 - - + +
61A GLY 5.0 7.0 - - - +
63A TYR* 4.7 18.8 - - + -
71A LEU* 2.9 44.4 + - + +
72A GLY* 3.6 9.0 - - - +
73A HIS 3.2 0.2 - - - -
74A SER* 1.3 75.1 - - - +
76A VAL* 1.3 64.3 + - - +
78A ILE* 3.4 7.5 + - + +
79A ALA* 3.2 18.4 + - - +
299A TYR 5.5 0.4 - - - +
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Residues in contact with VAL 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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61A GLY 5.8 0.9 - - - +
62A ILE* 5.0 7.2 - - + +
63A TYR* 3.7 32.1 - - + +
65A PRO* 4.0 8.3 - - + -
72A GLY 3.0 20.7 + - - +
73A HIS* 3.8 8.3 - - + +
74A SER 3.4 0.2 - - - -
75A MET* 1.3 73.0 - - - +
77A GLU* 1.3 57.1 + - - +
79A ALA* 2.8 11.1 + - - +
80A LYS* 2.8 57.5 + - + +
110A PHE* 3.9 16.8 - - + -
504A MRD 3.8 7.4 - - - +
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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 HIS* 3.1 13.4 + - - +
74A SER* 3.4 13.0 - - - +
76A VAL* 1.3 81.7 - - - +
78A ILE* 1.3 63.0 + - + +
80A LYS* 3.2 35.7 + - - +
81A GLN* 2.9 25.7 + - + +
301A LEU* 4.2 13.7 - - + -
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Residues in contact with ILE 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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39A ARG 3.4 26.9 - - - +
40A MET* 3.7 7.9 - - - -
41A ARG* 3.3 32.8 - - + +
59A THR* 5.2 0.2 - - - -
60A PRO* 3.6 13.9 - - + -
74A SER 3.0 20.5 + - - +
75A MET* 3.5 12.3 - - - +
76A VAL 3.2 0.2 - - - -
77A GLU* 1.3 75.5 - - - +
79A ALA* 1.3 63.0 + - - +
81A GLN* 3.5 4.0 + - - +
82A SER* 3.2 23.2 + - - +
299A TYR 4.1 9.4 - - - +
300A ALA 4.1 17.9 - - - +
301A LEU* 3.8 24.2 - - + +
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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
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9A VAL* 5.0 1.8 - - + -
59A THR* 4.1 17.8 - - + +
60A PRO 4.2 11.4 - - - +
62A ILE* 3.9 31.9 - - + -
75A MET 3.2 7.9 + - - +
76A VAL 2.8 10.2 + - - +
78A ILE* 1.3 78.2 - - - +
80A LYS* 1.3 67.2 + - - +
82A SER* 3.1 12.5 + - - -
83A LEU* 3.1 18.8 + - - +
110A PHE* 5.9 0.4 - - + -
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Residues in contact with LYS 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 VAL* 2.8 24.2 + - + +
77A GLU* 3.3 36.9 + - - +
79A ALA* 1.3 71.2 - - - +
81A GLN* 1.3 58.7 + - - +
83A LEU* 3.1 13.4 + - + +
84A GLU* 2.9 34.6 + - + +
110A PHE* 3.7 35.2 - - + -
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Residues in contact with GLN 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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41A ARG* 2.8 18.7 + - - +
77A GLU 2.9 8.2 + - - +
78A ILE 3.7 5.2 - - - +
79A ALA 3.1 0.2 - - - -
80A LYS* 1.3 74.9 - - - +
82A SER* 1.3 66.4 + - - +
84A GLU* 3.1 14.6 + - - +
85A GLU* 2.7 47.3 + - - +
301A LEU* 3.5 41.7 - - + +
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Residues in contact with SER 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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7A ALA* 3.6 8.4 - - - +
41A ARG* 4.7 11.4 - - - +
57A LEU* 3.9 31.8 - - - +
59A THR* 3.3 32.1 - - - +
78A ILE 3.2 13.1 + - - -
79A ALA 3.1 4.2 + - - -
81A GLN* 1.3 80.2 - - - +
83A LEU* 1.3 57.4 + - - +
85A GLU 3.4 0.9 + - - -
86A ALA* 3.0 29.5 + - - +
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Residues in contact with LEU 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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7A ALA* 4.4 3.8 - - + -
9A VAL* 3.9 35.4 - - + -
62A ILE* 4.7 6.7 - - + -
79A ALA 3.1 21.5 + - - +
80A LYS* 3.1 12.6 + - + +
82A SER* 1.3 77.1 - - - +
84A GLU* 1.3 53.9 + - - +
86A ALA* 3.3 8.7 + - - +
89A ILE* 3.4 36.1 - - + +
110A PHE* 3.8 31.6 - - + +
111A ILE* 4.7 2.2 - - + -
114A LEU* 3.9 15.6 - - + +
116A LYS* 2.6 34.0 + - - +
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Residues in contact with GLU 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 LYS* 2.9 23.2 + - + +
81A GLN* 3.3 17.5 - - - +
83A LEU* 1.3 77.5 - - - +
85A GLU* 1.3 57.8 + - - +
114A LEU* 4.2 22.1 - - - +
116A LYS* 2.9 16.8 + - - +
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Residues in contact with GLU 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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5A TYR* 3.4 56.2 + - + +
41A ARG* 2.8 18.8 + - - -
57A LEU* 4.5 4.3 - - + +
81A GLN* 2.7 37.0 + - - +
82A SER 4.1 3.6 - - - +
84A GLU* 1.3 76.7 - - - +
86A ALA* 1.3 64.0 + - - +
87A ASP* 3.6 3.5 + - - +
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Residues in contact with ALA 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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5A TYR* 3.6 8.7 - - - -
6A VAL 4.7 0.2 - - - -
7A ALA* 3.7 22.7 - - + +
82A SER 3.0 18.0 + - - +
83A LEU* 3.7 9.0 - - - +
84A GLU 3.3 1.2 - - - -
85A GLU* 1.3 79.1 - - - +
87A ASP* 1.3 59.7 + - - +
88A VAL 3.7 15.9 - - - +
89A ILE* 4.4 5.8 - - + -
116A LYS* 2.7 31.7 + - - +
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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