Contacts of the helix formed by residues 70 - 88 (chain A) in PDB entry 1C3Q
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A THR 4.8 2.2 - - - -
69A LEU* 1.3 75.5 - - - +
71A LYS* 1.3 64.9 + - - +
72A GLU* 3.4 9.0 + - - +
73A SER* 2.8 28.9 + - - -
74A VAL* 3.0 23.6 + - - +
103A PHE* 4.1 5.8 - - - -
48B ALA* 4.2 13.2 - - - -
72B GLU* 6.1 1.3 - - - -
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Residues in contact with LYS 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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70A SER* 1.3 72.7 - - - +
72A GLU* 1.3 65.2 + - + +
74A VAL* 3.6 4.5 + - - +
75A GLU* 3.2 23.0 + - - +
103A PHE* 4.0 14.9 - - + -
50B GLU* 3.6 27.0 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 6.1 1.4 - - - -
70A SER* 3.1 7.2 + - - +
71A LYS* 1.3 78.8 - - + +
73A SER* 1.3 60.8 + - - +
75A GLU* 3.3 17.2 + - - +
76A ALA* 3.0 27.2 + - - +
72C GLU* 4.3 19.0 - - - +
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Residues in contact with SER 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 4.7 6.2 - - - +
47A TYR* 5.5 5.2 - - - -
68A THR 4.7 1.0 + - - -
69A LEU* 3.5 9.7 - - - -
70A SER* 2.8 39.9 + - - -
72A GLU* 1.3 72.9 - - - +
74A VAL* 1.3 60.5 + - - +
76A ALA* 3.1 7.9 + - - +
77A MET* 2.8 46.3 + - - +
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Residues in contact with VAL 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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66A ILE* 5.2 1.3 - - + -
69A LEU* 3.9 21.8 - - + -
70A SER 3.0 23.0 + - - +
71A LYS* 3.9 4.0 - - - +
73A SER* 1.3 76.2 + - - +
75A GLU* 1.3 63.6 + - - +
77A MET* 3.1 22.7 + - - +
78A ILE* 3.1 29.8 + - + +
103A PHE* 4.7 3.4 - - + -
107A SER* 3.8 32.1 - - - +
110A ASP* 5.2 4.7 - - + +
111A ILE* 4.4 14.4 - - + -
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Residues in contact with GLU 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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49A LYS* 4.0 25.9 + - + +
71A LYS* 3.2 12.9 + - + +
72A GLU* 3.5 19.5 - - - +
74A VAL* 1.3 80.4 - - - +
76A ALA* 1.3 62.1 + - + +
78A ILE* 3.3 9.2 + - - +
79A ILE* 3.1 40.7 + - + +
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Residues in contact with ALA 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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23A ILE* 4.1 5.6 - - + +
47A TYR 3.2 27.4 - - - +
49A LYS* 4.6 8.5 - - + +
52A VAL* 3.6 14.4 - - + +
72A GLU 3.0 13.9 + - - +
73A SER* 3.5 10.1 - - - +
75A GLU* 1.3 76.2 - - - +
77A MET* 1.3 60.3 + - - +
79A ILE* 3.3 9.9 + - - -
80A ALA* 2.9 30.5 + - - +
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Residues in contact with MET 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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23A ILE* 3.6 36.8 - - + +
24A THR* 5.5 1.1 - - - +
64A LEU* 3.8 36.2 - - + +
65A ASN 3.4 25.6 - - - +
66A ILE* 4.0 16.2 - - + -
69A LEU* 5.1 2.7 - - + -
73A SER* 2.8 36.9 + - - +
74A VAL* 3.1 13.9 + - - +
76A ALA* 1.3 73.1 - - - +
78A ILE* 1.3 58.4 + - - +
80A ALA* 3.4 2.4 + - - +
81A GLY* 2.9 24.9 + - - -
111A ILE* 3.8 25.8 - - + -
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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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74A VAL* 3.1 28.1 + - + +
75A GLU* 3.7 10.5 - - - +
77A MET* 1.3 75.0 - - - +
79A ILE* 1.3 66.9 + - + +
81A GLY* 3.7 0.2 - - - -
82A LYS* 2.9 37.7 + - + +
110A ASP* 4.2 26.2 - - + +
111A ILE* 4.1 20.2 - - + -
114A GLU* 3.7 28.9 - - + -
115A VAL* 4.0 7.2 - - + +
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Residues in contact with ILE 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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49A LYS* 4.0 28.3 - - + +
52A VAL* 3.7 16.2 - - + -
53A ALA* 4.2 15.7 - - + +
75A GLU* 3.1 41.8 + - + +
76A ALA* 3.3 6.9 + - - +
78A ILE* 1.3 78.0 - - + +
80A ALA* 1.3 62.7 + - - +
82A LYS* 3.6 7.6 + - - +
83A SER* 3.2 21.5 + - - -
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Residues in contact with ALA 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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21A HIS* 4.6 0.2 - - + -
23A ILE* 3.6 23.6 - - + -
52A VAL* 3.8 27.4 - - + +
56A ALA* 3.6 5.0 - - + +
62A LEU* 3.4 15.7 - - + +
76A ALA 2.9 17.5 + - - +
77A MET 3.7 2.7 - - - +
79A ILE* 1.3 77.0 - - - +
81A GLY* 1.3 58.5 + - - +
83A SER* 3.3 1.5 + - - -
84A ALA* 2.9 28.9 + - - +
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Residues in contact with GLY 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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62A LEU* 3.5 13.4 - - - +
64A LEU* 5.0 0.2 - - - -
77A MET 2.9 16.6 + - - -
78A ILE 3.2 1.8 + - - -
80A ALA* 1.3 76.6 - - - +
82A LYS* 1.3 56.8 + - - +
84A ALA* 3.2 3.1 + - - +
85A ASN* 2.8 33.6 + - - +
91A VAL* 4.4 1.3 - - - -
115A VAL* 3.6 26.1 - - - +
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Residues in contact with LYS 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 ILE* 2.9 26.2 + - + +
79A ILE* 3.9 7.0 - - - +
81A GLY* 1.3 75.5 - - - +
83A SER* 1.3 63.1 + - - +
85A ASN* 3.3 10.3 + - - +
86A GLU* 3.0 23.4 + - - +
114A GLU* 2.8 65.5 + - - +
115A VAL* 4.2 0.4 - - - +
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Residues in contact with SER 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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53A ALA* 2.8 42.1 + - - +
56A ALA* 4.4 1.6 - - - -
57A LYS* 3.9 12.5 + - - +
79A ILE 3.2 13.0 + - - -
80A ALA 3.6 7.9 - - - -
82A LYS* 1.3 78.7 - - - +
84A ALA* 1.3 63.1 + - - +
86A GLU* 3.1 18.2 + - - +
87A HIS* 3.2 24.7 + - - +
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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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56A ALA* 4.3 8.7 - - + +
62A LEU* 4.0 9.6 - - + -
80A ALA 2.9 17.9 + - - +
81A GLY 3.5 5.4 - - - +
83A SER* 1.3 77.0 - - - +
85A ASN* 1.3 56.9 + - - +
87A HIS* 3.2 1.6 + - - -
88A GLY 2.9 9.4 + - - -
89A VAL* 2.9 58.9 + - + +
91A VAL* 3.6 13.5 - - + -
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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 GLY 2.8 22.6 + - - +
82A LYS* 3.5 10.9 - - - +
84A ALA* 1.3 76.1 - - - +
86A GLU* 1.3 63.4 + - - +
87A HIS 3.2 0.7 + - - -
88A GLY* 3.5 8.2 + - - -
89A VAL 4.9 1.7 - - - +
91A VAL* 4.1 6.1 - - - +
114A GLU 4.4 2.2 + - - -
115A VAL* 3.5 11.2 - - - +
116A ARG* 2.9 91.6 + - - +
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Residues in contact with GLU 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 LYS 3.0 13.2 + - - +
83A SER* 3.1 14.7 + - - +
85A ASN* 1.3 76.7 - - - +
87A HIS* 1.3 76.6 + - + +
88A GLY 3.7 0.2 - - - -
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Residues in contact with HIS 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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57A LYS* 3.7 42.2 - - + +
83A SER* 3.2 19.2 + - - +
84A ALA 3.2 4.4 + - - +
85A ASN 3.1 0.4 - - - -
86A GLU* 1.3 105.7 - - + +
88A GLY* 1.3 61.7 + - - +
89A VAL* 3.3 14.7 - - + +
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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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-10A ARG* 4.0 11.8 + - - -
84A ALA 2.9 4.3 + - - -
85A ASN* 3.5 9.6 + - - -
86A GLU 3.7 0.2 - - - -
87A HIS* 1.3 77.7 - - - +
89A VAL* 1.3 61.9 + - - +
90A PRO* 3.5 8.7 - - - +
116A ARG* 5.9 0.9 - - - -
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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