Contacts of the helix formed by residues 71 - 89 (chain A) in PDB entry 1EQ1
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 LYS 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY* 1.3 70.3 - - - -
72A ALA* 1.3 58.3 + - - +
73A LYS* 3.7 11.9 - - - +
74A GLU* 4.5 4.7 + - + +
75A ALA* 4.3 11.3 + - - +
131A GLU* 4.6 23.1 + - - +
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Residues in contact with ALA 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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68A ALA* 5.0 3.1 - - + -
70A GLY* 3.1 4.8 - - - +
71A LYS* 1.3 77.7 - - - +
73A LYS* 1.3 70.6 + - - +
74A GLU 2.7 3.8 + - - -
75A ALA* 2.9 7.2 + - + +
76A LEU* 2.8 28.2 + - + +
131A GLU* 4.3 16.6 - - + +
134A ASN* 4.7 6.3 - - + +
137A LEU* 3.4 30.1 - - + -
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Residues in contact with LYS 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 ILE* 2.8 56.3 - - + +
68A ALA* 3.3 27.9 - - + +
70A GLY 2.7 30.6 + - - +
71A LYS* 3.8 9.0 - - - +
72A ALA* 1.3 81.0 - - - +
74A GLU* 1.3 82.5 + - + +
76A LEU* 4.5 0.2 - - - -
77A GLU* 3.1 5.2 + - - +
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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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71A LYS* 4.7 5.8 - - - +
72A ALA 2.7 1.4 + - - -
73A LYS* 1.3 104.5 + - + +
75A ALA* 1.3 59.0 + - - +
76A LEU 3.0 1.1 - - - -
77A GLU* 2.7 37.9 + - - +
78A GLN* 3.2 6.9 + - - +
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Residues in contact with ALA 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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71A LYS 4.3 5.6 + - - +
72A ALA* 2.9 15.2 + - + +
74A GLU* 1.3 79.0 - - - +
76A LEU* 1.3 66.3 + - + +
77A GLU 3.4 0.2 + - - -
78A GLN* 3.5 13.3 + - - +
79A ALA* 3.5 13.3 + - - +
121A LYS* 5.2 5.5 + - - +
122A LEU* 5.1 1.6 - - - +
125A GLU* 4.1 31.0 - - + +
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Residues in contact with LEU 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 LEU* 3.9 14.4 - - + +
64A ALA* 3.3 17.7 - - + -
65A ILE* 3.0 28.0 - - + +
72A ALA* 2.8 16.0 + - + +
75A ALA* 1.3 79.4 - - + +
77A GLU* 1.3 63.8 + - - +
79A ALA* 4.2 3.6 - - - +
80A ARG* 3.4 20.6 + - - +
122A LEU* 3.5 41.3 - - + -
125A GLU* 6.0 1.3 - - + -
126A VAL* 4.8 2.5 - - + -
137A LEU* 2.9 47.3 - - + -
141A ILE* 4.6 0.4 - - + -
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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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65A ILE* 4.2 14.0 - - + +
73A LYS 3.1 14.9 + - - +
74A GLU* 2.7 21.8 + - - +
76A LEU* 1.3 78.1 - - - +
78A GLN* 1.3 61.0 + - - +
80A ARG* 3.4 18.3 + - - +
81A GLN* 3.2 48.8 + - - +
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Residues in contact with GLN 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 GLU 3.2 6.4 + - - +
75A ALA* 3.9 9.0 - - - +
76A LEU 3.3 0.2 - - - -
77A GLU* 1.3 75.5 - - - +
79A ALA* 1.3 57.0 + - - +
80A ARG 2.8 5.0 + - - -
81A GLN* 3.1 1.9 + - - -
82A ASN* 2.4 70.5 + - + +
121A LYS* 3.1 24.8 + - - +
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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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61A LEU* 4.2 6.0 - - + +
75A ALA 3.5 10.1 + - - +
76A LEU 4.3 1.1 - - - +
78A GLN* 1.3 78.4 + - - +
80A ARG* 1.3 49.9 + - - +
82A ASN* 4.1 3.6 - - - -
83A VAL* 2.6 51.4 - - + +
118A GLU* 5.2 6.7 - - + +
121A LYS* 5.0 6.1 - - + +
122A LEU* 3.1 43.1 - - + +
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Residues in contact with ARG 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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58A SER* 2.8 45.6 - - - +
59A SER* 3.9 4.7 - - - +
61A LEU* 4.4 4.5 - - + +
62A GLN* 3.8 37.5 + - - +
65A ILE* 5.3 1.2 - - - +
76A LEU 3.4 12.0 + - - +
77A GLU* 3.4 21.8 + - - +
78A GLN 2.8 1.6 + - - -
79A ALA* 1.3 78.2 - - - +
81A GLN* 1.3 90.6 + - - +
83A VAL* 3.2 0.5 - - - +
84A GLU* 3.0 38.6 + - - +
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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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77A GLU* 3.2 37.3 + - - +
78A GLN* 3.1 2.5 + - - +
80A ARG* 1.3 104.8 - - - +
82A ASN* 1.3 61.1 + - - +
84A GLU* 3.6 11.8 - - - +
85A LYS* 2.8 33.3 + - - +
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Residues in contact with ASN 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 GLN* 2.4 64.9 + - - +
79A ALA* 4.1 0.9 - - - -
81A GLN* 1.3 74.8 - - - +
83A VAL* 1.3 57.9 + - - +
85A LYS* 4.2 4.7 - - - +
86A THR* 3.3 17.8 + - - +
118A GLU* 2.6 45.1 + - - +
121A LYS* 4.8 1.6 - - - +
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Residues in contact with VAL 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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54A LEU* 4.1 6.4 - - - +
57A PHE* 3.2 40.2 - - + -
58A SER* 3.6 6.7 - - - -
79A ALA* 2.6 34.3 - - + +
80A ARG 3.2 7.0 - - - +
82A ASN* 1.3 73.9 - - - +
84A GLU* 1.3 64.5 + - - +
86A THR* 2.7 25.1 - - + +
87A ALA* 3.6 8.8 + - - +
115A THR* 4.5 5.3 + - + +
118A GLU* 3.2 38.4 - - + +
148A PHE* 5.8 1.1 - - + -
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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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55A SER* 3.3 27.9 + - - +
58A SER* 3.2 21.3 + - - +
59A SER* 5.1 4.3 + - - -
80A ARG* 3.0 31.2 + - - +
81A GLN* 3.1 12.4 + - - +
83A VAL* 1.3 80.7 - - - +
85A LYS* 1.3 58.7 + - - +
88A GLU* 2.7 38.3 + - + +
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Residues in contact with LYS 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 GLN 2.8 15.9 + - - +
82A ASN* 4.2 5.2 - - - +
84A GLU* 1.3 76.4 - - - +
86A THR* 1.3 59.9 + - - +
87A ALA 3.1 2.0 - - - -
88A GLU* 3.4 18.4 + - - +
89A GLU* 2.4 59.8 + - - +
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Residues in contact with THR 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 ASN* 3.3 8.0 + - - +
83A VAL* 2.7 44.6 - - - +
85A LYS* 1.3 82.5 - - - +
87A ALA* 1.3 62.6 + - - +
89A GLU* 3.3 14.9 - - - +
111A ALA* 2.6 34.5 + - - +
114A THR* 2.4 33.2 + - - -
115A THR* 3.6 16.6 - - - +
118A GLU* 4.1 5.2 - - - +
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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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51A LEU* 3.1 26.2 - - - +
54A LEU* 2.9 55.4 - - + -
55A SER* 3.5 7.2 - - - +
83A VAL 3.6 2.4 + - - +
85A LYS 3.1 0.4 - - - -
86A THR* 1.3 81.9 - - + +
88A GLU* 1.3 61.0 + - - +
89A GLU 2.9 8.4 + - - -
90A LEU* 3.7 6.8 + - - +
108A LEU* 5.7 0.4 - - - -
111A ALA* 4.3 7.9 - - - +
115A THR* 4.7 1.3 - - - +
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Residues in contact with GLU 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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51A LEU* 3.8 4.9 - - + +
55A SER* 3.8 7.8 + - - +
84A GLU* 2.7 31.2 + - + +
85A LYS* 3.4 18.9 + - - +
87A ALA* 1.3 76.5 - - - +
89A GLU* 1.3 67.6 + - - +
90A LEU 3.2 0.9 - - - -
91A ARG* 2.6 66.1 + - + +
92A LYS* 3.4 13.1 + - - +
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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
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85A LYS* 2.4 54.5 + - - +
86A THR* 3.3 18.1 - - - +
87A ALA 2.9 0.8 - - - -
88A GLU* 1.3 81.7 - - - +
90A LEU* 1.3 63.8 + - + +
92A LYS* 3.6 14.7 + - - +
107A LYS* 6.0 4.0 - - + -
111A ALA* 5.0 5.6 - - + +
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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