Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 2HTE
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 4.9 1.3 - - - -
56A LEU* 5.4 0.2 - - - -
57A THR* 2.7 27.1 + - - +
59A LYS* 1.3 78.5 - - + +
61A GLU* 1.3 68.0 + - - +
62A PHE* 3.2 8.5 - - + -
63A ALA* 3.1 17.6 + - + +
223A ILE* 3.3 23.2 - - + +
224A PRO* 3.4 24.1 - - + +
225A THR* 2.6 46.5 + - - +
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Residues in contact with GLU 61 (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* 4.3 12.1 - - + -
57A THR 3.2 19.6 + - - +
58A GLU* 4.2 10.2 + - - +
59A LYS 3.8 1.2 - - - -
60A ASP* 1.3 79.3 - - - +
62A PHE* 1.3 74.3 + - - +
63A ALA 3.1 1.0 + - - -
64A TYR* 3.1 5.4 + - - +
65A HIS* 2.7 61.6 + - + +
94A ARG* 2.7 39.8 + - - -
125A ILE* 3.9 24.8 - - + +
223A ILE* 4.5 5.8 - - - -
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Residues in contact with PHE 62 (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 GLU 4.9 3.4 - - - -
59A LYS 3.1 28.5 - - - -
60A ASP* 4.2 5.8 - - + -
61A GLU* 1.3 94.1 + - - +
63A ALA* 1.3 77.4 + - + +
66A GLU* 2.9 50.2 + - + +
94A ARG* 4.3 9.4 - - - +
259A LYS* 3.4 56.8 - - + -
260A TYR* 3.8 16.6 - + + -
3009A UNX 4.7 2.0 - - - -
3010A UNX 4.6 14.1 - - - -
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Residues in contact with ALA 63 (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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60A ASP* 3.1 14.0 + - + +
62A PHE* 1.3 91.6 - - + +
64A TYR* 1.3 63.4 + - - +
67A MET* 3.2 31.4 + - - +
221A ILE* 3.7 4.0 - - + +
222A SER 3.7 17.3 - - - +
223A ILE* 4.4 5.6 - - + -
224A PRO* 6.2 0.2 - - + -
260A TYR* 3.5 28.8 - - + -
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Residues in contact with TYR 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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60A ASP 4.0 0.2 + - - -
61A GLU* 3.1 4.9 + - - +
63A ALA* 1.3 79.2 - - - +
65A HIS* 1.3 92.3 + + - +
67A MET* 4.2 0.2 - - - +
68A MET* 3.1 68.3 + - + +
92A ILE* 5.0 0.4 - - + -
158A ASP* 2.8 30.6 + - - -
191A GLN* 3.1 24.9 + - + +
221A ILE* 4.0 12.3 - - + -
223A ILE* 3.7 21.8 - - + -
226A TYR* 3.6 24.7 - + - -
231A ILE* 3.7 28.7 - - + -
232A GLY 5.6 0.4 - - - -
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Residues in contact with HIS 65 (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 GLN 5.8 0.8 + - - -
56A LEU* 3.7 22.6 - - + +
61A GLU* 2.7 47.0 + - + +
64A TYR* 1.3 103.1 - + - +
66A GLU* 1.3 60.9 + - - +
69A THR* 2.7 31.9 + - - -
89A ASP* 3.3 27.1 + - - -
91A GLY* 3.6 25.0 - - - +
92A ILE* 3.7 24.3 - - + +
94A ARG* 4.1 5.8 - - - +
95A GLU* 3.8 3.3 - - + +
158A ASP* 4.1 3.5 + - - -
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Residues in contact with GLU 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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62A PHE* 2.9 37.3 + - - +
63A ALA 4.3 0.9 - - - +
65A HIS* 1.3 72.8 - - - +
67A MET* 1.3 56.8 + - - +
70A HIS* 2.9 46.7 + - + +
95A GLU* 3.7 24.2 - - - +
98A LYS* 5.2 1.4 + - - -
257A ASP 4.5 0.5 - - - +
258A LEU* 3.6 17.2 - - + +
259A LYS* 2.8 30.3 + - - +
260A TYR* 2.8 24.7 + - + -
261A TYR* 2.9 19.4 + - + +
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Residues in contact with MET 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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63A ALA 3.2 19.4 + - - +
66A GLU* 1.3 74.7 - - - +
68A MET* 1.3 62.1 + - - +
71A VAL* 3.3 50.6 + - + +
220A ASN 5.3 0.4 - - - +
221A ILE* 3.7 25.1 - - + -
233A ILE* 4.1 7.0 - - + +
260A TYR* 3.4 41.5 - - + -
261A TYR* 3.8 22.9 - - - -
265A ASN* 3.9 14.1 - - - +
266A HIS* 4.4 3.4 - - - -
269A ALA* 3.8 28.9 - - + -
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Residues in contact with MET 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 TYR* 3.1 63.4 + - + +
67A MET* 1.3 76.2 - - - +
69A THR* 1.3 57.8 + - - +
72A PRO* 3.2 18.7 - - - +
92A ILE* 3.6 13.7 - - + -
156A ILE* 3.7 22.6 - - + +
157A VAL 3.7 21.8 - - - +
158A ASP* 4.2 3.4 - - + -
189A VAL* 3.2 18.7 - - - +
190A ALA 4.5 1.3 - - - -
191A GLN* 4.0 12.1 - - - +
221A ILE* 4.2 4.7 - - + -
232A GLY 5.2 0.4 - - - +
233A ILE* 3.7 32.5 - - - -
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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 HIS 2.7 22.3 + - - -
66A GLU 4.0 0.7 - - - -
68A MET* 1.3 76.6 - - - +
70A HIS* 1.3 66.1 + - + +
71A VAL 3.4 0.4 - - - -
72A PRO* 3.2 13.3 - - - +
73A MET* 3.1 26.5 + - + +
92A ILE* 3.3 21.3 - - - +
95A GLU* 3.6 29.8 - - + +
96A LEU* 3.5 36.1 - - + +
99A TYR* 4.4 0.2 - - + -
156A ILE* 4.1 5.8 - - - -
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Residues in contact with HIS 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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66A GLU* 2.9 40.1 + - + +
69A THR* 1.3 75.6 - - + +
71A VAL* 1.3 56.7 + - - +
73A MET 3.9 0.7 - - - -
74A THR* 2.6 36.9 + - - +
95A GLU* 2.8 43.6 + - + +
98A LYS* 4.7 0.2 - - + -
99A TYR* 2.8 43.1 + + - +
250A LEU* 3.9 7.7 - - + +
255A PHE* 3.9 13.7 - + - -
258A LEU* 3.6 14.6 - - + +
261A TYR* 3.7 27.2 + - + -
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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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67A MET* 3.3 44.5 + - + +
70A HIS* 1.3 82.3 - - - +
72A PRO* 1.4 69.2 - - + +
74A THR* 3.1 9.9 + - - -
75A VAL* 3.4 6.8 - - - +
189A VAL* 4.8 1.3 - - + -
219A ALA* 6.0 0.2 - - + -
233A ILE* 4.6 9.6 - - + -
235A CYS* 4.5 9.2 - - - -
243A LEU* 3.9 16.2 - - + +
261A TYR* 4.0 2.9 - - + -
266A HIS* 3.2 39.9 - - + +
270A PHE* 3.9 19.5 - - + -
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Residues in contact with PRO 72 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A MET 3.2 22.0 - - - +
69A THR 3.2 20.9 - - - +
71A VAL* 1.4 90.3 - - + +
73A MET* 1.3 50.4 + - - +
75A VAL* 3.1 2.4 + - - +
76A SER* 2.8 37.4 + - - -
154A VAL* 3.7 28.2 - - + +
156A ILE* 4.4 2.7 - - + -
187A TYR* 4.6 5.1 - - + -
189A VAL* 3.8 26.7 - - + -
243A LEU* 3.6 18.4 - - + +
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Residues in contact with MET 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* 3.1 21.5 + - + +
71A VAL 3.3 0.2 - - - -
72A PRO* 1.3 79.6 - - + +
74A THR* 1.3 52.0 + - - +
76A SER* 3.7 4.1 - - - +
79A PRO* 3.5 28.6 - - + +
82A VAL* 3.9 14.4 - - - -
96A LEU* 3.7 26.9 - - + -
99A TYR* 3.2 49.5 - - + +
102A VAL* 3.6 25.1 - - + -
154A VAL* 3.9 14.4 - - + -
248A LYS* 2.7 31.9 + - - -
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Residues in contact with THR 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 HIS 2.6 25.9 + - - +
71A VAL 3.1 7.3 + - - -
73A MET* 1.3 77.2 - - - +
75A VAL* 1.3 54.6 + - - +
99A TYR* 3.9 3.6 - - - +
246A PRO* 3.8 7.9 - - - -
247A ASN* 2.7 35.7 + - - +
248A LYS* 3.4 25.0 + - + +
250A LEU* 3.8 35.9 - - + -
261A TYR* 3.1 22.0 + - + +
266A HIS* 3.2 8.8 + - - -
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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