Contacts of the helix formed by residues 16 - 33 (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 THR 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLU* 4.9 1.7 + - - +
15B GLN* 1.3 85.0 - - + +
17B GLU* 1.3 64.2 + - - +
18B GLU* 3.9 7.1 + - - +
19B ALA* 3.2 24.3 + - - +
20B ARG* 3.2 26.8 + - - +
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Residues in contact with GLU 17 (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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16B THR* 1.3 70.6 - - - +
18B GLU* 1.3 62.0 + - - +
20B ARG* 3.2 11.5 + - - +
21B ARG* 2.8 33.7 + - + +
24B ARG* 3.0 31.3 + - - -
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Residues in contact with GLU 18 (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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16B THR* 3.3 7.9 + - - +
17B GLU* 1.3 79.8 - - - +
19B ALA* 1.3 56.8 + - - +
21B ARG* 2.7 45.9 + - - +
22B ALA* 2.9 31.8 + - + +
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Residues in contact with ALA 19 (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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12B GLU* 3.5 34.3 - - + +
14B PHE* 3.7 19.6 - - + -
16B THR* 3.2 21.9 + - - +
18B GLU* 1.3 78.2 - - - +
20B ARG* 1.3 58.3 + - - +
22B ALA* 3.3 6.8 + - - +
23B MET* 2.9 28.4 + - - +
114B ARG* 4.7 3.7 - - - +
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Residues in contact with ARG 20 (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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14B PHE* 2.8 35.1 + - + +
15B GLN* 4.4 25.0 + - - +
16B THR 3.2 10.7 + - - +
17B GLU* 3.2 15.5 + - - +
19B ALA* 1.3 72.7 - - - +
21B ARG* 1.3 60.8 + - - +
23B MET* 3.2 2.8 + - - +
24B ARG* 2.9 52.6 + - - +
128B TRP* 4.2 18.3 - - + -
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Residues in contact with ARG 21 (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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17B GLU* 2.8 25.7 + - + +
18B GLU* 2.7 45.3 + - - +
20B ARG* 1.3 73.4 - - - +
22B ALA* 1.3 69.2 + - - +
24B ARG* 3.3 25.5 + - - +
25B GLU* 3.0 59.7 + - - +
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Residues in contact with ALA 22 (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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18B GLU* 2.9 30.2 + - + +
19B ALA* 3.6 7.9 - - - +
21B ARG* 1.3 87.0 - - - +
23B MET* 1.3 57.9 + - - +
25B GLU* 3.5 10.4 + - - +
26B ALA* 3.0 27.9 + - - +
114B ARG* 4.1 24.9 - - + +
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Residues in contact with MET 23 (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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14B PHE* 3.8 18.6 - - + -
19B ALA 2.9 16.8 + - - +
20B ARG 3.6 4.5 - - - +
22B ALA* 1.3 74.9 - - - +
24B ARG* 1.3 59.8 + - - +
26B ALA* 3.1 2.1 + - - -
27B LEU* 2.8 39.6 + - + +
114B ARG* 4.1 17.2 - - - +
117B GLU* 3.9 33.9 - - + +
118B ALA* 4.5 4.3 - - - +
121B VAL* 4.2 10.8 - - + -
128B TRP* 3.7 61.2 - - + +
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Residues in contact with ARG 24 (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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17B GLU* 3.0 29.7 + - - -
20B ARG* 2.9 40.4 + - - +
21B ARG* 3.4 27.8 - - - +
23B MET* 1.3 75.2 - - - +
25B GLU* 1.3 57.3 + - - +
27B LEU* 3.4 10.8 + - + +
28B ARG* 3.0 29.7 + - - +
31B ARG* 4.8 2.4 + - - -
128B TRP* 4.5 14.9 - - + -
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Residues in contact with GLU 25 (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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21B ARG* 3.0 42.5 + - + +
22B ALA* 3.5 11.6 - - - +
24B ARG* 1.3 76.2 - - - +
26B ALA* 1.3 57.7 + - - +
28B ARG* 3.3 8.2 + - - +
29B ARG* 3.0 28.8 + - + +
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Residues in contact with ALA 26 (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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22B ALA 3.0 18.1 + - - +
23B MET* 3.1 4.9 + - - +
25B GLU* 1.3 75.9 - - + +
27B LEU* 1.3 59.3 - - - +
29B ARG* 3.3 5.6 + - - +
30B VAL* 2.9 35.2 + - - +
114B ARG* 3.5 41.3 - - + +
115B GLU* 3.9 5.6 - - + +
118B ALA* 3.8 3.4 - - + -
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Residues in contact with LEU 27 (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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23B MET* 2.8 31.3 + - + +
24B ARG* 3.7 10.1 - - + +
26B ALA* 1.3 71.2 - - - +
28B ARG* 1.3 64.1 + - - +
30B VAL 3.5 0.2 + - - -
31B ARG* 3.0 34.0 + - - +
118B ALA* 3.8 20.2 - - + +
121B VAL* 4.0 24.5 - - + -
122B TYR* 3.5 35.7 - - + +
128B TRP* 3.9 28.3 - - + +
355B GLU* 4.2 13.9 - - + +
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Residues in contact with ARG 28 (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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24B ARG 3.0 15.5 + - - +
25B GLU* 3.5 10.2 - - - +
27B LEU* 1.3 77.8 - - - +
29B ARG* 1.3 63.6 + - - +
31B ARG* 3.4 30.2 + - - +
32B GLU* 3.0 52.4 + - + +
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Residues in contact with ARG 29 (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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25B GLU* 3.0 17.9 + - + +
26B ALA* 3.3 7.4 + - - +
28B ARG* 1.3 75.0 - - - +
30B VAL* 1.3 64.7 + - + +
32B GLU* 3.3 14.2 + - + +
33B GLU* 3.2 48.0 + - + +
36B ARG* 5.6 1.6 - - - +
112B ARG* 5.6 1.6 - - - +
115B GLU* 3.3 49.6 + - + +
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Residues in contact with VAL 30 (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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26B ALA 2.9 20.8 + - - +
27B LEU 3.9 2.9 - - - +
29B ARG* 1.3 77.0 - - + +
31B ARG* 1.3 59.4 + - - +
33B GLU* 3.0 23.6 + - - +
34B PHE* 3.4 18.7 + - + -
115B GLU* 3.6 36.3 - - + +
118B ALA* 3.7 7.6 - - + -
119B THR* 3.6 24.0 - - + +
122B TYR* 3.9 19.5 - - + -
218B LYS* 4.0 14.0 + - - +
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Residues in contact with ARG 31 (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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24B ARG 4.8 2.2 + - - -
27B LEU* 3.0 32.3 + - - +
28B ARG* 3.4 39.4 - - - +
30B VAL* 1.3 72.5 - - - +
32B GLU* 1.3 67.5 + - + +
33B GLU 3.1 1.6 - - - -
34B PHE* 3.2 51.6 + - + +
122B TYR* 3.1 28.2 + - + -
355B GLU* 4.1 6.5 + - - -
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Residues in contact with GLU 32 (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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28B ARG* 3.0 47.9 + - + +
29B ARG* 3.6 14.1 - - + +
30B VAL 3.3 0.2 - - - -
31B ARG* 1.3 78.3 - - + +
33B GLU* 1.3 60.4 + - + +
34B PHE 3.4 1.0 + - - -
35B GLY 4.8 1.7 + - - -
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Residues in contact with GLU 33 (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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29B ARG* 3.2 46.3 + - + +
30B VAL* 3.0 14.2 + - - +
32B GLU* 1.3 80.9 - - + +
34B PHE* 1.3 63.9 + - - +
35B GLY 3.1 3.1 - - - -
36B ARG* 3.0 62.3 + - - +
38B TYR* 4.3 5.1 + - - +
65B VAL 4.4 2.2 - - - +
115B GLU* 4.7 2.1 - - - +
218B LYS* 4.6 10.9 + - - +
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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