Contacts of the helix formed by residues 72 - 91 (chain B) in PDB entry 2EIT
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LYS 3.8 1.6 + - - -
71B ALA* 1.3 74.4 - - - +
73B LYS* 1.3 67.0 + - - -
74B ALA 3.3 2.9 - - - -
75B GLU* 2.9 14.9 + - - -
76B ALA* 3.0 22.1 + - - +
242B GLU* 5.5 5.8 - - - -
243B VAL* 4.3 9.2 - - - +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY* 1.3 71.0 - - - -
74B ALA* 1.3 57.1 + - - +
76B ALA* 3.2 9.7 + - - +
77B GLU* 2.9 34.1 + - - +
242B GLU 5.6 4.5 - - - +
243B VAL* 5.7 0.2 - - - +
246B TYR* 3.7 48.5 - - + +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 3.3 0.6 - - - -
73B LYS* 1.3 79.3 - - - +
75B GLU* 1.3 68.8 + - - +
77B GLU* 3.4 7.5 + - - +
78B ALA* 3.0 27.2 + - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.6 32.8 - - + -
42B ILE* 4.0 9.6 - - + +
47B VAL* 5.7 4.0 - - + -
49B THR* 3.9 17.3 - - + +
70B LYS 4.5 0.6 - - - +
71B ALA* 4.0 8.1 - - + -
72B GLY* 2.9 29.4 + - - +
74B ALA* 1.3 84.7 + - - +
76B ALA* 1.3 60.0 + - - +
78B ALA* 3.6 8.4 - - - +
79B ALA* 2.9 30.7 + - - +
236B LEU* 4.0 3.6 - - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY 3.0 14.0 + - - +
73B LYS* 3.4 7.9 - - - +
75B GLU* 1.3 75.7 - - - +
77B GLU* 1.3 57.0 + - - +
79B ALA* 3.3 3.1 + - - +
80B LEU* 2.9 30.4 + - - +
236B LEU* 3.6 11.5 - - + +
243B VAL* 3.8 19.3 - - + -
246B TYR* 3.7 24.5 - - + -
247B LEU* 4.2 14.2 - - + +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 2.9 14.5 + - + +
74B ALA* 3.6 10.3 - - - +
76B ALA* 1.3 73.5 - - - +
78B ALA* 1.3 65.5 + - - +
80B LEU* 3.2 8.1 + - - +
81B GLU* 3.0 25.8 + - - +
246B TYR* 2.2 36.0 + - + +
250B HIS* 2.6 30.6 + - - -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.0 15.6 - - + +
74B ALA 3.0 17.3 + - - +
75B GLU* 3.4 9.4 + - - +
77B GLU* 1.3 75.7 - - - +
79B ALA* 1.3 58.8 + - - +
81B GLU* 3.5 8.6 + - - +
82B ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.7 16.1 - - + +
75B GLU 2.9 18.5 + - - +
76B ALA 3.7 4.3 - - - +
78B ALA* 1.3 75.6 - - - +
80B LEU* 1.3 54.1 + - - +
82B ALA* 3.2 2.7 + - - +
83B ALA* 2.8 36.9 + - - +
205B ILE* 3.7 16.8 - - + -
234B ASN* 4.1 13.8 + - + -
236B LEU* 3.9 20.6 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ALA 2.9 14.0 + - - +
77B GLU* 3.2 10.3 + - - +
79B ALA* 1.3 74.1 - - - +
81B GLU* 1.3 60.0 + - - +
83B ALA* 3.3 1.1 + - - +
84B TRP* 2.9 66.1 + - + +
176B ALA* 4.4 5.6 - - + -
205B ILE* 3.5 14.7 - - + +
247B LEU* 4.1 11.2 - - + -
250B HIS* 3.3 50.7 - - + +
252B ARG* 3.7 12.8 - - + +
253B ILE* 3.8 18.6 - - + -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 3.0 15.6 + - - +
78B ALA* 3.6 8.9 - - - +
80B LEU* 1.3 77.1 - - - +
82B ALA* 1.3 61.9 + - - +
84B TRP* 4.0 3.7 - - - +
85B LYS* 3.0 28.7 + - + +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 4.2 5.6 - - + -
43B GLY* 3.9 31.2 - - - +
78B ALA 3.0 16.9 + - - +
79B ALA 3.2 4.7 + - - +
81B GLU* 1.3 78.1 - - - +
83B ALA* 1.3 57.3 - - - +
85B LYS* 3.4 6.7 + - - +
86B ALA* 3.0 30.0 + - - +
230B PRO 4.5 0.3 - - - +
231B GLY* 3.6 7.2 - - - -
234B ASN* 4.2 1.3 - - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 2.8 17.1 + - - +
80B LEU* 3.8 3.6 - - - +
81B GLU 3.2 0.2 - - - -
82B ALA* 1.3 75.7 - - - +
84B TRP* 1.3 59.7 + - - +
86B ALA 3.4 0.3 + - - -
87B PHE* 2.9 19.4 + - - +
176B ALA* 3.7 13.0 - - + -
203B THR* 2.8 32.2 + - - +
204B VAL 4.9 2.0 - - - +
205B ILE* 4.3 11.0 - - + -
231B GLY 3.3 17.9 + - - +
234B ASN* 3.9 7.6 - - - +
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Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.9 42.3 + - + +
81B GLU* 4.1 4.3 - - - +
83B ALA* 1.3 73.2 - - - +
85B LYS* 1.3 67.5 + - - +
87B PHE* 3.2 32.2 + + + +
88B LYS* 3.3 25.1 + - + +
174B LEU 4.3 4.3 - - - -
175B GLY* 3.6 20.2 - - - -
176B ALA* 3.5 29.8 - - + +
252B ARG* 2.8 41.5 + - + +
254B ARG* 4.2 4.9 - - + -
281B TRP* 3.5 30.5 - + - -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.0 22.3 + - + +
82B ALA* 3.7 7.0 - - - +
84B TRP* 1.3 77.8 - - - +
86B ALA* 1.3 62.2 + - - +
88B LYS* 3.5 33.2 + - + +
89B THR* 4.3 5.2 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ALA 3.0 15.2 + - - +
83B ALA 3.7 2.9 - - - +
85B LYS* 1.3 74.8 - - - +
87B PHE* 1.3 61.2 + - - +
89B THR* 3.1 8.9 + - - -
90B TRP* 2.9 27.9 + - - +
203B THR* 4.1 2.7 - - + -
229B PRO* 5.8 0.9 - - + -
230B PRO 3.2 26.2 - - - +
231B GLY 3.5 17.0 - - - -
232B VAL* 3.7 10.5 - - + +
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 2.9 18.3 + - - +
84B TRP* 3.2 31.4 + + + +
86B ALA* 1.3 77.4 - - - +
88B LYS* 1.3 68.4 + - + +
89B THR 3.0 1.4 + - - -
90B TRP* 4.4 1.3 - - - -
91B LYS* 3.1 47.5 + - + +
173B PRO* 3.6 25.1 - - + -
174B LEU 3.9 2.9 - - - -
175B GLY* 3.4 40.4 - - - -
201B GLY 3.2 26.7 - - - -
202B ASN* 4.3 1.1 - - - -
203B THR* 3.7 12.1 - - - +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B TRP* 3.5 20.6 - - + +
85B LYS* 3.6 26.5 - - + +
86B ALA 3.2 0.6 - - - -
87B PHE* 1.3 81.7 - - + +
89B THR* 1.3 63.4 + - + +
91B LYS* 3.6 27.1 - - - +
92B ASP* 3.7 8.1 - - - +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS 4.7 3.8 + - - +
86B ALA* 3.1 9.4 + - - -
87B PHE 3.1 0.2 - - - -
88B LYS* 1.3 82.9 - - + +
90B TRP* 1.3 63.5 + - - +
91B LYS 3.2 1.8 - - - -
92B ASP* 2.9 25.5 + - - +
93B TRP* 3.3 19.4 + - - -
229B PRO* 6.0 1.7 - - - +
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Residues in contact with TRP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ALA 2.9 18.8 + - - +
87B PHE* 4.3 2.2 - - - +
89B THR* 1.3 78.3 + - - +
91B LYS* 1.3 62.3 + - - +
92B ASP 3.1 1.0 + - - -
93B TRP* 3.1 51.8 + + - +
98B ARG* 3.1 42.3 + - + -
101B LEU* 3.6 18.4 - - + -
102B LEU* 5.5 0.2 - - + -
198B VAL* 3.0 41.9 + - + -
199B ALA* 5.3 0.4 - - - -
201B GLY* 3.3 21.1 - - - -
202B ASN 3.2 23.3 + - - -
203B THR* 4.0 4.9 - - + -
228B PHE* 4.1 7.9 - + - -
229B PRO* 3.7 26.7 - - + -
232B VAL* 3.7 21.5 - - + +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ARG 4.5 4.2 + - - -
463A GLU* 3.1 32.0 + - - -
1520A ACT 5.5 4.0 + - - +
87B PHE* 3.1 45.5 + - + +
88B LYS* 3.6 20.9 - - - +
90B TRP* 1.3 76.4 - - - +
92B ASP* 1.3 85.2 + - - +
93B TRP 3.4 0.9 - - - +
98B ARG* 3.2 15.9 + - - +
173B PRO* 3.7 28.2 - - + +
201B GLY 3.9 8.6 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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