Contacts of the helix formed by residues 72 - 91 (chain A) in PDB entry 2EHQ
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 GLY 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.6 2.9 + - - -
71A ALA* 1.3 75.5 - - - +
73A LYS* 1.3 65.7 + - - -
74A ALA 3.3 2.5 - - - -
75A GLU* 2.8 15.6 + - - -
76A ALA* 2.9 22.3 + - - +
243A VAL* 3.7 9.5 - - - +
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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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72A GLY* 1.3 71.7 - - - -
74A ALA* 1.3 57.2 + - - +
76A ALA* 3.2 8.4 + - - +
77A GLU* 2.8 34.5 + - + +
242A GLU 6.0 1.3 - - - -
243A VAL* 5.1 2.0 - - + +
246A TYR* 3.6 49.8 - - + +
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Residues in contact with ALA 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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72A GLY 3.3 0.6 - - - -
73A LYS* 1.3 77.6 - - - +
75A GLU* 1.3 71.2 + - - +
77A GLU* 3.3 8.3 + - - +
78A ALA* 3.0 26.9 + - - +
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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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40A LEU* 3.5 33.2 - - + -
42A ILE* 3.9 9.3 - - + +
47A VAL* 5.7 3.6 - - + -
49A THR* 4.1 17.5 - - + +
70A LYS 4.3 1.2 - - - +
71A ALA* 4.0 9.2 - - + -
72A GLY* 2.8 33.3 + - - +
74A ALA* 1.3 85.2 + - - +
76A ALA* 1.3 59.9 + - - +
78A ALA* 3.3 8.2 + - - +
79A ALA* 2.9 30.3 + - - +
236A LEU* 4.2 2.5 - - - -
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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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72A GLY 2.9 13.8 + - - +
73A LYS 3.4 8.1 - - - +
75A GLU* 1.3 76.5 - - - +
77A GLU* 1.3 56.6 + - - +
79A ALA* 3.3 2.9 + - - +
80A LEU* 2.9 34.5 + - - +
236A LEU* 3.7 12.9 - - + +
243A VAL* 3.8 19.1 - - + -
246A TYR* 3.8 20.6 - - + -
247A LEU* 4.1 14.3 - - + +
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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 LYS* 2.8 18.7 + - + +
74A ALA* 3.6 10.1 - - - +
76A ALA* 1.3 73.7 - - - +
78A ALA* 1.3 65.1 + - - +
80A LEU* 3.2 6.5 + - - +
81A GLU* 3.0 33.8 + - + +
246A TYR* 2.6 28.6 + - + +
250A HIS* 2.8 27.9 + - - -
252A ARG* 4.1 15.8 + - - -
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Residues in contact with ALA 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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42A ILE* 3.9 16.7 - - + +
74A ALA 3.0 14.9 + - - +
75A GLU* 3.3 11.9 + - - +
77A GLU* 1.3 75.7 - - - +
79A ALA* 1.3 58.1 + - - +
81A GLU* 3.4 8.1 + - - +
82A ALA* 3.0 27.9 + - - +
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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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42A ILE* 3.8 13.4 - - + +
75A GLU 2.9 17.2 + - - +
76A ALA 3.6 4.5 - - - +
77A GLU 3.2 0.2 - - - -
78A ALA* 1.3 74.3 - - - +
80A LEU* 1.3 59.3 + - - +
82A ALA* 3.3 2.6 + - - +
83A ALA* 2.8 32.1 + - - +
205A ILE* 3.9 18.4 - - + +
234A ASN* 4.2 12.3 + - + -
236A LEU* 3.9 24.5 - - + -
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Residues in contact with LEU 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 ALA 2.9 14.6 + - - +
77A GLU* 3.2 15.9 + - - +
79A ALA* 1.3 76.5 - - - +
81A GLU* 1.3 63.6 + - - +
83A ALA* 3.8 0.4 - - - -
84A TRP* 2.9 45.5 + - + +
176A ALA* 5.0 1.8 - - + -
205A ILE* 3.7 13.4 - - + +
246A TYR* 5.4 0.4 - - + -
247A LEU* 4.0 11.9 - - + -
250A HIS* 3.4 44.6 - - + +
252A ARG* 3.8 31.9 - - + +
253A ILE* 3.8 20.9 - - + -
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Residues in contact with GLU 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* 3.0 23.4 + - + +
78A ALA* 3.8 6.5 - - - +
80A LEU* 1.3 75.4 - - - +
82A ALA* 1.3 58.1 + - - +
84A TRP* 3.9 0.9 - - - +
85A LYS* 3.0 32.4 + - - +
252A ARG* 3.0 37.1 + - - +
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Residues in contact with ALA 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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42A ILE* 4.3 3.6 - - + -
43A GLY* 3.9 32.5 - - - +
78A ALA 3.0 17.2 + - - +
79A ALA 3.7 4.3 - - - +
81A GLU* 1.3 75.3 - - - +
83A ALA* 1.3 57.9 + - - +
85A LYS* 3.5 6.7 + - - +
86A ALA* 2.9 30.8 + - - +
230A PRO 4.5 0.2 - - - +
231A GLY* 3.6 7.9 - - - -
234A ASN* 4.1 2.2 - - - +
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Residues in contact with ALA 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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79A ALA 2.8 21.0 + - - +
80A LEU 3.8 2.2 - - - +
82A ALA* 1.3 74.9 - - - +
84A TRP* 1.3 57.5 + - - +
86A ALA 3.4 0.2 + - - -
87A PHE* 2.9 19.6 + - - +
176A ALA* 3.7 13.2 - - + -
203A THR* 2.8 30.7 + - - +
204A VAL 4.9 1.6 - - - +
205A ILE* 4.3 11.9 - - + -
231A GLY 3.3 17.0 + - - +
234A ASN* 3.9 8.3 - - - +
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Residues in contact with TRP 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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80A LEU* 2.9 34.0 + - + +
81A GLU 4.2 1.8 - - - +
83A ALA* 1.3 74.8 - - - +
85A LYS* 1.3 67.6 + - - +
87A PHE* 3.3 32.0 + + - +
88A LYS* 3.4 13.8 + - - +
174A LEU 4.3 3.6 - - - -
175A GLY* 3.6 20.2 - - - -
176A ALA* 3.5 35.8 - - + +
252A ARG* 2.7 55.9 + - + +
254A ARG* 4.2 4.3 - - + -
281A TRP* 3.5 30.3 - + - -
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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 GLU 3.0 18.8 + - - +
82A ALA* 3.8 7.4 - - - +
84A TRP* 1.3 77.4 - - - +
86A ALA* 1.3 61.3 + - - +
88A LYS* 3.4 31.1 + - - +
89A THR* 4.2 5.0 + - - +
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Residues in contact with ALA 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 ALA 2.9 15.2 + - - +
83A ALA 3.8 1.8 - - - +
85A LYS* 1.3 74.6 - - - +
87A PHE* 1.3 61.2 + - - +
89A THR* 3.1 9.5 + - - -
90A TRP* 2.8 28.2 + - - +
203A THR* 4.1 2.9 - - + -
229A PRO* 5.9 0.4 - - + -
230A PRO 3.2 27.4 - - - +
231A GLY 3.5 16.2 - - - +
232A VAL* 3.7 12.1 - - + +
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Residues in contact with PHE 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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83A ALA 2.9 19.2 + - - +
84A TRP* 3.3 30.9 + + + +
86A ALA* 1.3 75.5 - - - +
88A LYS* 1.3 66.7 + - - +
90A TRP* 4.4 1.3 - - - -
91A LYS* 3.0 53.4 + - + +
173A PRO* 3.6 26.7 - - + -
174A LEU 3.8 3.1 - - - -
175A GLY* 3.5 41.5 - - - -
201A GLY 3.2 27.4 - - - -
202A ASN* 4.2 1.3 - - - -
203A THR* 3.6 13.4 - - + +
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Residues in contact with LYS 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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84A TRP 3.4 6.6 + - - +
85A LYS* 3.5 30.4 + - - +
86A ALA 3.2 0.6 - - - -
87A PHE* 1.3 82.8 - - - +
89A THR* 1.3 64.1 + - + +
91A LYS* 3.5 27.8 - - - +
92A ASP* 3.7 8.7 - - - +
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Residues in contact with THR 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 4.4 3.8 + - - +
86A ALA* 3.1 9.9 + - - -
88A LYS* 1.3 86.3 - - + +
90A TRP* 1.3 66.3 + - - +
91A LYS 3.2 1.8 - - - -
92A ASP* 3.0 18.6 + - - +
93A TRP* 3.4 18.6 + - - -
229A PRO* 6.1 0.9 - - - +
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Residues in contact with TRP 90 (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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86A ALA 2.8 23.7 + - - +
87A PHE* 4.3 1.8 - - - +
89A THR* 1.3 74.3 + - - +
91A LYS* 1.3 57.5 + - - +
92A ASP 3.2 1.2 + - - -
93A TRP* 3.2 48.5 + + - +
98A ARG* 3.0 52.1 + - + -
101A LEU* 3.8 17.3 - - + -
102A LEU* 5.4 0.4 - - + -
198A VAL* 3.0 37.3 + - + -
199A ALA* 5.3 0.4 - - - -
201A GLY* 3.3 21.5 - - - -
202A ASN 3.1 23.2 + - - -
203A THR* 4.0 5.2 - - + -
228A PHE* 4.0 9.2 - + - -
229A PRO* 3.7 27.6 - - + -
232A VAL* 3.6 21.9 - - + +
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Residues in contact with LYS 91 (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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87A PHE* 3.0 48.6 + - + +
88A LYS* 3.5 24.2 - - - +
90A TRP* 1.3 77.8 - - - +
92A ASP* 1.3 79.4 + - - +
93A TRP 3.4 0.9 - - - +
98A ARG* 3.2 17.0 + - - +
173A PRO* 3.7 27.8 - - + +
201A GLY 3.8 7.5 + - - -
462B ARG 4.7 4.8 + - - -
463B GLU* 3.4 27.2 + - - -
2520B ACT 5.5 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