Contacts of the helix formed by residues 27 - 39 (chain B) in PDB entry 1MWT
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 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS* 1.3 56.0 + - - +
29B GLU* 2.6 24.2 + - + -
30B ILE* 2.8 31.1 + - + -
31B ASN* 3.2 15.6 + - - +
85B ILE* 3.7 27.1 - - + +
93B LYS* 2.8 31.3 + - - -
123B TRP* 5.4 0.9 + - + -
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Residues in contact with LYS 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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27B ASP* 1.3 73.2 - - - +
29B GLU* 1.3 57.5 + - - +
31B ASN* 3.6 9.6 + - + +
32B ASN* 2.8 51.2 + - - +
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Residues in contact with GLU 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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27B ASP* 2.6 12.0 + - + +
28B LYS* 1.3 72.1 - - - +
30B ILE* 1.3 80.9 + - + +
31B ASN 3.1 1.3 - - - -
32B ASN* 2.8 21.7 + - - +
33B THR* 3.0 14.4 + - - -
122B MET* 3.6 25.2 - - - +
123B TRP* 3.2 39.5 + - + -
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Residues in contact with ILE 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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27B ASP* 2.8 24.0 + - + +
29B GLU* 1.3 79.2 - - + +
31B ASN* 1.3 62.8 + - - +
33B THR* 3.2 7.2 + - - -
34B ILE* 3.1 25.2 + - + +
85B ILE* 4.7 11.0 - - + -
93B LYS* 3.4 44.6 - - + +
95B VAL* 4.3 13.5 - - + -
116B PHE* 3.5 34.9 - - + -
123B TRP* 4.2 31.4 - - + -
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Residues in contact with ASN 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 ASP 3.2 20.8 + - - +
28B LYS* 3.7 12.0 - - - +
29B GLU 3.1 0.2 - - - -
30B ILE* 1.3 78.7 - - - +
32B ASN* 1.3 53.1 + - - +
34B ILE* 3.1 4.4 + - - -
35B ASP* 2.6 48.9 + - - +
83B ARG* 2.9 41.3 + - - +
85B ILE* 4.2 18.8 - - - +
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Residues in contact with ASN 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 LYS* 2.8 41.8 + - - +
29B GLU* 2.8 18.2 + - - +
31B ASN* 1.3 77.0 - - - +
33B THR* 1.3 55.5 + - - +
35B ASP* 3.3 14.8 + - - +
36B ALA* 2.8 28.9 + - - +
48B ASP* 5.5 1.1 - - - +
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Residues in contact with THR 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 GLU 3.0 9.3 + - - -
30B ILE* 3.5 8.4 - - - -
32B ASN* 1.3 76.0 - - - +
34B ILE* 1.3 65.1 + - - +
36B ALA* 3.0 22.6 + - - +
37B ILE* 3.0 15.6 + - + +
45B VAL* 4.4 9.4 - - + +
48B ASP* 3.4 34.3 + - + +
116B PHE* 4.3 13.8 - - + -
123B TRP 5.2 3.1 + - - -
125B LEU* 3.9 32.3 - - + -
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Residues in contact with ILE 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 ILE* 3.1 19.6 + - + +
31B ASN* 3.1 4.1 + - - +
33B THR* 1.3 77.0 - - + +
35B ASP* 1.3 60.8 + - - +
37B ILE* 3.1 20.8 + - + +
38B GLU* 3.2 12.0 + - - +
80B ILE* 3.8 24.2 - - + +
83B ARG* 3.3 43.5 - - - +
85B ILE* 6.2 0.9 - - + -
95B VAL* 3.8 37.0 - - + -
114B PHE* 3.9 18.2 - - + -
116B PHE* 4.3 8.7 - - + -
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Residues in contact with ASP 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 ASN* 2.6 40.6 + - - +
32B ASN* 3.6 16.0 + - - +
34B ILE* 1.3 72.5 - - - +
36B ALA* 1.3 55.0 + - - +
38B GLU* 2.9 16.3 + - - +
39B ASP* 2.6 44.6 + - - +
83B ARG* 2.7 32.0 + - - -
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Residues in contact with ALA 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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32B ASN 2.8 14.6 + - - +
33B THR* 3.0 17.5 - - - +
35B ASP* 1.3 76.5 - - - +
37B ILE* 1.3 54.1 + - - +
39B ASP* 3.3 8.0 + - - -
40B LYS 2.9 22.2 + - - -
41B ASN* 3.0 19.4 + - + +
44B GLN* 4.4 22.0 - - + -
45B VAL* 3.9 15.8 - - + +
48B ASP* 5.1 0.4 - - - +
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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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33B THR* 3.0 16.7 + - + +
34B ILE* 3.3 17.9 - - + +
36B ALA* 1.3 77.2 - - - +
38B GLU* 1.3 61.9 + - - +
40B LYS* 3.0 17.8 + - - +
42B PHE* 5.3 4.5 - - + -
45B VAL* 4.0 15.7 - - + -
70B TYR* 5.0 2.5 + - - +
78B ILE* 4.0 6.2 - - - +
80B ILE* 4.0 10.5 - - + -
99B TYR* 3.5 24.7 - - + +
114B PHE* 3.7 34.1 - - + -
116B PHE* 6.5 0.2 - - + -
125B LEU* 5.3 3.8 - - + -
131B VAL* 3.6 31.9 - - + +
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Residues in contact with GLU 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 ILE 3.2 9.2 + - - +
35B ASP* 2.9 17.2 + - - +
37B ILE* 1.3 79.2 - - - +
39B ASP* 1.3 65.4 + - - +
40B LYS* 3.2 7.2 + - - +
78B ILE* 3.7 36.9 + - + +
79B ASN* 4.0 7.1 - - - +
80B ILE* 2.7 42.4 + - + +
81B GLN* 4.0 4.1 + - - -
83B ARG* 2.4 32.1 + - - -
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Residues in contact with ASP 39 (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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35B ASP* 2.6 32.7 + - - +
36B ALA* 3.3 7.8 + - - +
37B ILE 3.2 0.2 - - - -
38B GLU* 1.3 81.4 - - - +
40B LYS* 1.3 75.1 + - - +
41B ASN* 3.2 8.4 + - + +
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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