Contacts of the helix formed by residues 63 - 80 (chain A) in PDB entry 4ZEQ
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.4 2.1 + - - +
62A VAL* 1.3 82.4 - - - +
64A VAL* 1.3 58.8 + - - +
65A ASP* 3.5 10.3 + - - +
66A THR* 2.6 31.0 + - - -
67A ALA 2.9 23.2 + - - -
103A LEU* 3.7 16.3 - - - +
107A GLN* 4.5 5.6 - - - +
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Residues in contact with VAL 64 (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 SER* 1.3 74.9 - - - +
65A ASP* 1.3 55.1 + - - +
67A ALA* 3.3 7.2 + - - +
68A ARG* 2.7 50.2 + - - +
103A LEU* 4.1 6.2 - - + +
107A GLN* 3.9 6.8 - - - +
114A THR* 3.7 35.0 - - + -
117A GLU* 3.7 40.2 - - + +
118A ILE* 4.2 10.1 - - + -
121A PHE* 4.3 3.4 - - + -
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 3.2 8.6 + - - +
64A VAL* 1.3 78.1 - - - +
66A THR* 1.3 59.3 + - - +
68A ARG* 3.0 25.4 + - - +
69A THR* 3.0 39.4 + - + +
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Residues in contact with THR 66 (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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59A VAL* 5.8 4.3 - - + -
60A ASN 3.2 26.7 - - - +
61A VAL* 4.0 7.0 - - + -
62A VAL* 3.5 13.1 - - + +
63A SER* 2.6 38.5 + - - -
65A ASP* 1.3 76.2 - - - +
67A ALA* 1.3 56.2 + - - +
69A THR* 3.1 7.7 + - - +
70A LEU* 3.0 34.3 + - + +
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Residues in contact with ALA 67 (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 VAL* 3.8 20.6 - - + +
63A SER 2.9 13.1 + - - +
64A VAL* 3.5 8.3 - - - +
66A THR* 1.3 76.7 - - - +
68A ARG* 1.3 57.1 + - - +
70A LEU* 4.6 2.9 - - - -
71A PHE* 2.8 33.1 + - - +
99A LEU* 3.8 15.1 - - + +
103A LEU* 4.9 2.2 - - + -
118A ILE* 3.6 25.1 - - + -
121A PHE* 3.8 4.0 - - + -
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Residues in contact with ARG 68 (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 VAL* 2.7 29.7 + - - +
65A ASP* 3.0 39.9 + - - +
67A ALA* 1.3 73.6 - - - +
69A THR* 1.3 62.1 + - + +
71A PHE* 3.4 1.2 + - - +
72A ASN* 2.9 51.3 + - - +
117A GLU* 4.9 8.3 + - - +
120A TYR* 6.4 0.2 - - - -
121A PHE* 3.5 40.1 - - + +
124A GLU* 5.9 0.4 + - - -
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Residues in contact with THR 69 (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 ASP* 3.0 24.2 + - + +
66A THR* 3.1 11.1 + - - +
68A ARG* 1.3 77.5 - - + +
70A LEU* 1.3 61.7 + - - +
72A ASN* 3.4 5.7 + - - +
73A GLN* 2.9 46.1 + - - +
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Residues in contact with LEU 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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56A LEU* 6.3 0.7 - - + -
59A VAL* 4.2 28.9 - - + -
61A VAL* 4.2 16.8 - - + -
66A THR* 3.0 21.0 + - + +
67A ALA 3.8 2.2 - - - +
69A THR* 1.3 76.2 + - - +
71A PHE* 1.3 63.2 + - - +
73A GLN* 4.0 7.2 + - - +
74A VAL* 3.0 39.9 + - + +
95A PHE* 4.1 12.1 - - + -
99A LEU* 3.5 24.2 - - + -
102A LYS* 5.8 0.7 - - + -
82B ILE* 5.3 0.7 - - + -
83B ILE* 3.2 30.1 - - + -
86B ILE* 4.7 8.7 - - + -
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Residues in contact with PHE 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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67A ALA 2.8 22.6 + - - +
68A ARG 3.6 2.7 - - - +
70A LEU* 1.3 75.2 - - - +
72A ASN* 1.3 70.5 + - - +
74A VAL* 3.3 1.2 + - - +
75A MET* 2.8 60.2 + - + +
92A ILE* 3.8 30.7 - - + -
95A PHE* 3.9 24.5 - + - -
96A GLU* 4.9 1.8 - - + -
99A LEU* 3.7 11.2 - - + +
121A PHE* 3.5 30.3 - + + -
122A VAL* 3.7 24.9 - - + -
125A PHE* 3.7 22.7 - - + -
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Residues in contact with ASN 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 ARG* 2.9 40.6 + - - +
69A THR* 3.4 5.9 + - - +
71A PHE* 1.3 93.8 - - - +
73A GLN* 1.3 59.1 + - + +
75A MET* 3.8 3.7 - - - +
76A GLU* 2.9 30.9 + - - +
121A PHE* 4.9 5.5 - - - +
125A PHE* 4.9 10.1 - - - +
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Residues in contact with GLN 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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69A THR* 2.9 31.7 + - - +
70A LEU* 4.0 4.1 - - - +
72A ASN* 1.3 77.6 - - + +
74A VAL* 1.3 60.8 + - - +
76A GLU* 3.5 11.2 + - - +
77A LYS* 3.2 30.4 + - - +
83B ILE* 3.8 33.8 - - + +
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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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70A LEU* 3.0 41.4 + - + +
71A PHE 3.7 2.5 - - - +
73A GLN* 1.3 72.9 - - - +
75A MET* 1.3 67.4 + - + +
77A LYS 3.3 1.4 + - - -
78A GLU* 2.8 26.9 + - - +
95A PHE* 4.0 14.4 - - + -
83B ILE* 4.0 21.8 - - + +
86B ILE* 3.8 15.9 - - + -
87B ALA* 3.4 13.3 - - - +
90B LEU* 3.8 29.2 - - + -
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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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71A PHE* 2.8 53.1 + - + +
72A ASN* 3.8 4.3 - - - +
74A VAL* 1.3 85.3 - - + +
76A GLU* 1.3 65.6 + - - +
78A GLU* 3.2 26.3 + - - +
79A PHE* 3.1 31.1 + - - +
92A ILE* 3.7 34.1 - - - -
95A PHE* 4.2 13.7 - - + -
125A PHE* 3.6 32.4 - - + -
90B LEU* 4.2 7.4 - - + -
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Residues in contact with GLU 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 ASN 2.9 19.1 + - - +
73A GLN* 3.7 11.4 - - - +
74A VAL 3.3 0.2 - - - -
75A MET* 1.3 75.2 - - - +
77A LYS* 1.3 78.4 + - - +
79A PHE* 3.8 1.9 - - - +
80A GLU* 3.0 34.5 + - + +
125A PHE* 4.7 4.9 - - - -
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Residues in contact with LYS 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 GLN* 3.2 15.5 + - - +
76A GLU* 1.3 99.3 + - - +
78A GLU* 1.3 64.9 + - - +
80A GLU* 3.3 41.7 + - - +
83B ILE* 4.1 14.8 - - + +
84B ARG* 4.1 28.9 - - + +
87B ALA* 3.4 22.9 - - + +
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Residues in contact with GLU 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 2.8 16.2 + - - +
75A MET* 3.2 31.0 + - - +
77A LYS* 1.3 78.5 - - - +
79A PHE* 1.3 74.1 + - + +
80A GLU 3.7 0.3 + - - -
81A ASP* 4.2 3.5 - - - +
88A ARG* 3.2 29.4 + - - +
91A THR* 2.6 27.2 + - - -
87B ALA* 3.5 15.4 - - + +
90B LEU* 3.5 24.8 - - - +
91B ALA* 3.6 25.3 + - + +
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Residues in contact with PHE 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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75A MET* 3.1 22.7 + - - +
76A GLU* 3.8 1.8 - - - +
78A GLU* 1.3 95.4 - - + +
80A GLU* 1.3 64.7 + - - +
81A ASP* 3.2 3.6 - - - -
82A GLY* 3.0 17.7 + - - -
83A ILE 3.6 16.8 - - - -
84A ILE* 4.4 16.4 - - + -
88A ARG* 3.7 42.2 - - + +
89A ILE* 4.6 0.7 - - + -
92A ILE* 3.7 25.1 - - + -
125A PHE* 3.7 28.5 - + + -
129A ASN* 6.3 0.9 - - + -
130A THR* 4.3 15.0 - - + -
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Residues in contact with GLU 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 GLU* 3.0 17.9 + - + +
77A LYS* 3.3 42.0 + - - +
78A GLU 3.4 1.0 - - - -
79A PHE* 1.3 77.4 - - - +
81A ASP* 1.3 64.2 + - + +
82A GLY* 3.2 2.1 + - - -
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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