Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 5XRZ
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 GLU 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR 4.7 1.6 + - - -
53A SER* 3.5 17.2 + - - +
65A TYR* 3.7 12.5 - - + -
66A ILE* 1.3 77.8 - - - +
68A GLY* 1.3 66.9 + - - +
69A HIS* 2.7 37.8 + - + +
70A ARG* 3.2 38.7 + - + +
71A VAL* 3.3 6.6 - - - +
167B LEU 4.0 2.8 - - - +
169B LYS* 3.7 36.7 + - - +
2L T 3.5 20.0 - - - +
3L T 6.2 0.2 - - - +
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Residues in contact with GLY 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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67A GLU* 1.3 71.6 - - - +
69A HIS* 1.3 64.2 + - - +
71A VAL* 3.0 7.0 + - - +
72A ILE* 2.9 29.6 + - - +
148A THR* 4.2 21.1 - - - -
152A LYS* 4.5 8.1 - - - -
167B LEU* 6.4 0.2 - - - -
2L T 3.4 19.5 + - - -
3L T 5.8 0.4 - - - -
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Residues in contact with HIS 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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67A GLU* 2.7 36.3 + - + -
68A GLY* 1.3 72.4 - - - +
70A ARG* 1.3 88.6 + - + +
72A ILE* 4.1 2.7 - - - +
73A ASN* 2.9 41.6 + - - +
164B ASN* 3.4 38.5 + - - +
167B LEU* 3.3 38.7 + - + +
168B ASP* 3.6 33.8 - - - +
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Residues in contact with ARG 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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50A GLU 3.6 14.0 + - - -
51A TYR* 2.5 62.9 + - + +
52A ILE 4.6 0.6 + - - -
53A SER* 4.0 11.5 + - - -
66A ILE* 3.7 13.5 - - + -
67A GLU* 3.2 36.0 + - + +
68A GLY 3.1 0.6 - - - -
69A HIS* 1.3 97.6 - - + +
71A VAL* 1.3 56.4 + - - +
73A ASN* 3.3 5.8 + - - +
74A LEU* 2.9 35.9 + - + +
184A LEU* 6.2 1.0 - - - +
168B ASP* 4.4 13.1 + - - -
170B ASP* 4.6 10.3 + - - -
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Residues in contact with VAL 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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66A ILE* 3.6 22.2 - - + -
67A GLU 3.3 15.7 - - - +
68A GLY 3.0 4.4 + - - +
70A ARG* 1.3 74.5 - - - +
72A ILE* 1.3 58.6 + - + +
74A LEU* 3.3 8.4 + - + +
75A ALA* 2.9 29.1 + - - +
152A LYS* 4.1 30.1 - - + +
155A LEU* 3.8 27.4 - - + -
162A LEU* 4.0 26.7 - - + +
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Residues in contact with ILE 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 GLY* 2.9 19.7 + - - +
69A HIS 3.6 7.2 - - - +
71A VAL* 1.3 78.2 - - + +
73A ASN* 1.3 54.0 + - - +
75A ALA* 3.3 4.2 + - - +
76A ASN* 2.7 52.8 + - - +
84A TRP* 4.8 5.2 - - + -
148A THR* 6.3 2.5 - - + -
151A LEU* 4.4 21.8 - - + -
155A LEU* 5.5 0.9 - - + -
156B ARG* 4.6 4.0 - - + +
157B SER* 4.1 34.3 - - - +
159B GLY 5.3 0.2 - - - +
164B ASN* 3.3 31.2 - - + +
167B LEU* 6.6 0.4 - - + -
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Residues in contact with ASN 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 HIS* 2.9 32.2 + - - +
70A ARG* 3.8 5.6 - - - +
72A ILE* 1.3 72.8 - - - +
74A LEU* 1.3 66.8 + - - +
76A ASN* 3.3 5.5 + - - +
77A GLU* 2.9 34.5 + - + +
46B ARG* 5.9 2.6 - - - +
159B GLY* 4.9 2.6 - - - -
160B ASN* 2.8 38.1 + - - +
164B ASN* 2.8 20.2 + - - +
195K ASP* 4.4 20.7 + - - +
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Residues in contact with LEU 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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47A LEU* 4.4 10.5 - - + -
51A TYR* 4.3 24.9 - - + +
66A ILE* 5.0 11.0 - - + -
70A ARG* 2.9 25.7 + - + +
71A VAL* 3.3 14.1 + - + +
73A ASN* 1.3 77.7 - - - +
75A ALA* 1.3 56.9 + - - +
77A GLU* 3.8 4.0 - - - +
78A MET* 2.9 35.9 + - + +
161A ALA* 3.9 19.5 - - + +
162A LEU* 3.7 18.4 - - + -
192K LYS* 3.7 34.5 - - + +
195K ASP* 5.0 5.4 - - - +
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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 VAL 2.9 17.5 + - - +
72A ILE 3.7 3.6 - - - +
74A LEU* 1.3 76.5 - - - +
76A ASN* 1.3 63.9 + - - +
79A PHE* 3.0 35.4 + - + +
80A GLY 3.7 1.6 + - - -
84A TRP* 4.0 27.8 - - + -
155A LEU* 4.2 23.3 - - + -
162A LEU* 3.8 9.6 - - + +
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Residues in contact with ASN 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 ILE* 2.7 41.7 + - - +
73A ASN* 3.9 8.2 - - - +
75A ALA* 1.3 76.4 - - - +
77A GLU* 1.3 61.5 + - - +
80A GLY* 3.1 29.2 - - - -
81A TYR* 3.5 13.2 + - + +
84A TRP* 3.0 20.4 + - - +
40B GLN* 3.4 13.1 + - - +
157B SER 3.3 21.8 + - - +
158B PHE* 3.3 24.7 - - - +
159B GLY* 4.4 4.5 - - - +
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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 ASN* 2.9 24.3 + - + +
74A LEU* 3.8 4.5 - - - +
76A ASN* 1.3 83.4 - - - +
78A MET* 1.3 67.1 + - + +
79A PHE 3.3 0.2 - - - -
40B GLN* 4.1 4.8 + - - +
44B ARG* 2.8 53.3 + - - +
160B ASN* 5.8 1.2 + - - -
192K LYS* 6.2 0.4 - - - -
195K ASP* 3.7 41.0 - - + +
196K LEU* 4.1 9.9 - - - +
197K GLU* 5.0 8.9 + - + +
200K VAL* 5.1 0.7 - - - +
204K ARG* 2.9 18.7 + - - -
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Residues in contact with MET 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 ILE* 3.6 48.2 - - + +
42A ALA* 3.6 28.5 - - + +
43A LEU* 3.7 25.4 - - + -
74A LEU* 2.9 23.0 + - + +
77A GLU* 1.3 76.1 - - + +
79A PHE* 1.3 72.4 + - + +
161A ALA* 5.0 4.9 - - + -
162A LEU* 4.6 6.7 - - + -
192K LYS* 5.1 10.1 - - - -
197K GLU* 4.3 15.7 - - - -
200K VAL* 3.6 13.4 - - + +
204K ARG* 2.4 19.8 + - - -
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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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31A TYR* 3.6 20.0 - - - +
35A GLU* 5.0 0.2 - - - +
39A ILE* 4.2 9.4 - - + -
43A LEU* 4.4 11.4 - - + -
75A ALA* 3.0 21.1 + - + +
78A MET* 1.3 85.3 - - + +
80A GLY* 1.3 59.4 + - - +
82A ASN* 5.4 0.2 - - - +
83A GLY* 3.5 31.3 - - - -
84A TRP* 4.1 10.3 - - + +
115A LEU* 3.6 34.8 - - + -
116A LYS* 4.2 4.0 + - - -
155A LEU* 5.3 1.1 - - + -
158A PHE* 4.2 14.4 - + - -
162A LEU* 3.6 31.4 - - + -
81K TYR* 3.8 16.4 - + - -
204K ARG* 3.2 25.9 + - - +
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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