Contacts of the helix formed by residues 25 - 38 (chain B) in PDB entry 1EF1
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ASN* 4.0 8.1 - - - +
24B THR* 1.3 79.0 - - - +
26B GLY* 1.3 64.4 + - - +
27B LYS* 3.4 5.9 + - - +
28B GLN* 2.9 45.9 + - + +
29B LEU 3.3 8.8 + - - -
61B LEU 3.8 8.3 - - - -
62B ASN 4.8 5.6 - - - +
63B LYS 3.1 19.7 - - - +
64B LYS* 3.6 2.9 - - + +
65B VAL* 3.6 5.7 - - - +
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Residues in contact with GLY 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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25B THR* 1.3 70.5 - - - +
27B LYS* 1.3 57.0 + - - +
29B LEU* 3.3 3.5 + - - +
30B PHE* 2.9 29.8 + - - +
59B LEU* 3.3 29.3 - - - +
60B LYS 3.6 11.0 - - - -
61B LEU* 3.5 8.3 + - - +
63B LYS 2.8 14.1 + - - -
65B VAL* 4.0 5.7 - - - +
68B GLN* 4.4 0.2 - - - +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR* 3.2 5.4 - - - +
26B GLY* 1.3 76.8 - - - +
28B GLN* 1.3 65.2 + - + +
30B PHE* 3.8 6.3 - - + +
31B ASP* 3.1 60.4 + - - +
61B LEU* 2.9 43.0 + - + +
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Residues in contact with GLN 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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21B GLN* 5.0 8.5 - - - +
23B ASN* 3.8 12.7 + - - +
24B THR* 3.3 22.0 + - + +
25B THR* 2.9 42.9 + - + +
27B LYS* 1.3 81.9 - - + +
29B LEU* 1.3 62.5 + - - +
31B ASP* 3.5 8.7 + - - +
32B GLN* 3.2 28.0 + - - +
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Residues in contact with LEU 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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7B VAL* 4.2 11.2 - - + -
9B VAL* 4.7 3.8 - - + -
18B PHE* 4.1 23.1 - - + -
20B ILE* 4.1 20.6 - - + -
24B THR* 3.9 8.4 - - + +
25B THR 3.3 9.5 + - - +
26B GLY 3.6 7.2 - - - +
28B GLN* 1.3 78.5 - - - +
30B PHE* 1.3 62.2 + - - +
32B GLN* 3.2 13.8 + - - +
33B VAL* 3.1 21.3 + - + +
47B LEU* 3.8 20.4 - - + -
59B LEU* 4.3 6.1 - - + -
65B VAL* 4.4 9.0 - - + -
78B PHE* 3.7 36.8 - - + -
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Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 2.9 16.4 + - - +
27B LYS* 3.8 9.9 - - + +
29B LEU* 1.3 74.6 - - - +
31B ASP* 1.3 69.0 + - - +
33B VAL* 3.3 5.2 + - - +
34B VAL* 2.9 49.0 + - + +
42B VAL* 3.6 39.5 - - + -
45B PHE* 3.5 23.6 - - + -
46B GLY* 3.9 4.9 - - - -
47B LEU* 4.0 21.9 - - + +
61B LEU* 3.8 27.1 - - + -
80B PHE* 3.6 23.8 - + - -
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Residues in contact with ASP 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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27B LYS* 3.1 53.4 + - - +
28B GLN* 3.7 8.5 - - - +
29B LEU 3.2 0.2 - - - -
30B PHE* 1.3 83.3 - - - +
32B GLN* 1.3 59.7 + - + +
34B VAL* 3.6 10.3 - - - +
35B LYS* 2.8 35.1 + - + +
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Residues in contact with GLN 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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18B PHE* 3.3 39.2 - - + +
19B ALA 5.1 4.7 + - - +
20B ILE* 4.0 23.8 - - - +
24B THR* 5.0 3.6 - - - +
28B GLN* 3.2 16.3 + - - +
29B LEU* 3.2 13.1 + - - +
31B ASP* 1.3 78.4 - - + +
33B VAL* 1.3 53.5 + - - +
35B LYS* 3.4 5.5 - - - +
36B THR* 2.8 40.2 + - - +
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Residues in contact with VAL 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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9B VAL* 4.1 29.6 - - + -
11B THR* 5.0 2.0 - - + -
16B LEU* 4.2 8.3 - - + -
18B PHE* 3.7 23.1 - - + -
29B LEU* 3.1 17.9 - - + +
30B PHE* 3.3 10.1 - - - +
32B GLN* 1.3 73.0 - - - +
34B VAL* 1.3 68.3 + - - +
36B THR* 3.2 2.4 + - - -
37B ILE* 3.0 32.0 + - + +
47B LEU* 4.5 5.4 - - + -
80B PHE* 3.6 38.1 - - + -
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Residues in contact with VAL 34 (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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30B PHE* 2.9 50.1 + - + +
31B ASP* 3.6 14.8 - - + +
33B VAL* 1.3 73.1 - - - +
35B LYS* 1.3 68.1 + - - +
37B ILE* 3.5 8.1 + - - +
38B GLY 3.0 9.5 + - - -
39B LEU* 2.9 45.7 + - + +
42B VAL* 3.9 18.8 - - + -
80B PHE* 3.8 20.4 - - + -
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Residues in contact with LYS 35 (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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31B ASP* 2.8 23.9 + - + +
32B GLN* 3.4 7.4 - - - +
34B VAL* 1.3 89.1 + - - +
36B THR* 1.3 63.2 + - - +
38B GLY* 3.2 13.2 + - - -
39B LEU 5.1 2.8 + - - -
40B ARG* 6.0 4.9 - - - +
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Residues in contact with THR 36 (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 LEU* 3.6 34.5 - - + -
18B PHE* 3.4 16.0 - - + -
32B GLN* 2.8 25.9 + - - +
33B VAL 3.6 3.8 - - - -
35B LYS* 1.3 75.8 - - - +
37B ILE* 1.3 59.1 + - + +
38B GLY 3.6 0.2 + - - -
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Residues in contact with ILE 37 (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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11B THR* 4.3 16.6 - - + +
14B ALA* 5.6 4.7 - - + -
16B LEU* 3.9 27.1 - - + -
33B VAL* 3.0 21.8 + - + +
34B VAL* 3.6 8.1 - - - +
36B THR* 1.3 77.1 - - + +
38B GLY* 1.3 59.7 + - - +
39B LEU* 3.8 20.0 - - + -
80B PHE* 3.9 26.0 - - + -
97B ILE* 4.0 24.2 - - + +
101B LEU* 4.1 15.0 - - + -
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Residues in contact with GLY 38 (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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34B VAL 3.0 6.0 + - - -
35B LYS 3.2 10.6 + - - -
36B THR 3.3 1.0 + - - -
37B ILE* 1.3 78.6 - - - +
39B LEU* 1.3 59.0 + - - +
40B ARG* 3.7 18.7 + - - -
95B GLN* 3.0 22.2 + - - -
97B ILE* 3.8 4.9 - - - +
3001B SO4 5.2 0.2 + - - -
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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