Contacts of the helix formed by residues 36 - 44 (chain B) in PDB entry 1MTL
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 ARG 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA 4.2 2.5 - - - +
35B ASN* 1.3 75.2 + - - +
37B PHE* 1.3 54.3 + - - +
38B TRP 3.4 1.6 - - - -
39B LYS* 3.3 21.4 + - + +
40B VAL* 2.7 46.2 + - + +
141B PRO* 3.0 21.9 + - + +
142B SER 3.0 17.1 + - - -
145B SER* 2.8 32.3 + - - -
147B VAL* 2.9 21.3 + - - +
149B LEU* 3.7 14.1 - - + +
152B LEU* 3.5 16.6 - - - +
224D G 2.8 62.9 + - - +
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Residues in contact with PHE 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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14B PHE* 3.6 47.6 - + + -
30B PHE* 3.4 45.8 - + + -
35B ASN* 2.8 24.3 + - - +
36B ARG* 1.3 70.9 - - - +
38B TRP* 1.3 91.9 + + - +
40B VAL* 3.0 2.9 + - - +
41B ILE* 2.8 53.9 + - + +
59B LEU* 4.4 1.1 - - + -
66B VAL* 4.3 9.0 - - + -
107B LEU* 4.6 3.6 - - + -
141B PRO* 3.4 19.8 - - + +
156B TYR* 4.7 4.7 - + - -
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Residues in contact with TRP 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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29B PRO* 3.2 27.5 + - + -
30B PHE* 2.8 33.2 + - + +
35B ASN 4.8 7.9 - - - +
36B ARG 3.4 0.2 - - - -
37B PHE* 1.3 96.2 - + + +
39B LYS* 1.3 63.3 + - - +
41B ILE* 3.5 10.5 - - + +
42B TYR* 3.1 23.0 + - - +
50B GLN* 3.7 12.0 - - + +
51B LEU* 3.6 44.4 + - + +
52B LYS 4.8 0.2 - - - -
53B PRO* 3.6 28.1 - - + +
56B ALA* 3.8 19.1 - - + -
59B LEU* 3.5 39.3 - - + -
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Residues in contact with LYS 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 ASN 5.5 0.4 + - - +
36B ARG* 3.3 22.9 + - - +
37B PHE 3.3 0.4 - - - -
38B TRP* 1.3 78.9 - - - +
40B VAL* 1.3 57.6 + - - +
42B TYR* 3.3 1.8 + - - +
43B GLN* 2.9 57.9 + - + +
50B GLN* 3.4 36.2 + - - +
149B LEU* 4.0 25.3 - - + +
222D G 4.7 5.1 - - - +
223D C 2.8 45.2 + - - +
224D G 5.3 0.6 + - - -
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Residues in contact with VAL 40 (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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36B ARG* 2.7 31.7 + - + +
37B PHE* 3.5 4.7 - - - +
39B LYS* 1.3 72.7 - - - +
41B ILE* 1.3 52.7 + - - +
43B GLN* 3.5 0.9 - - - +
44B ALA* 2.6 38.1 + - - +
141B PRO* 4.9 1.1 - - + -
149B LEU* 4.0 11.7 - - + -
152B LEU* 3.8 40.8 - - + +
153B VAL* 4.3 10.2 - - + +
156B TYR* 3.5 45.3 - - + -
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Residues in contact with ILE 41 (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* 4.2 17.3 - - + -
37B PHE* 2.8 57.8 + - + +
38B TRP* 3.5 20.4 - - + +
40B VAL* 1.3 71.1 - - - +
42B TYR* 1.3 71.1 + - - +
44B ALA* 3.3 1.0 + - - -
45B GLY 3.0 4.2 + - - -
46B PHE* 3.0 40.2 + - + -
47B THR* 3.8 24.7 - - + +
51B LEU* 5.8 1.6 - - + +
59B LEU* 3.8 21.5 - - + -
156B TYR* 4.2 11.4 - - + -
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Residues in contact with TYR 42 (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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38B TRP 3.1 14.1 + - - +
39B LYS 3.5 5.6 - - - +
41B ILE* 1.3 74.1 - - - +
43B GLN* 1.3 78.4 + - + +
45B GLY* 2.6 30.3 + - - -
47B THR* 3.4 13.3 - - - +
48B ASP 3.5 22.0 - - - -
49B ARG* 3.6 35.0 - - - +
50B GLN* 3.9 24.2 - - + -
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Residues in contact with GLN 43 (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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39B LYS* 2.9 50.0 + - + +
40B VAL 3.9 2.2 - - - +
42B TYR* 1.3 92.8 - - + +
44B ALA* 1.3 59.2 + - - +
45B GLY 3.2 0.6 + - - -
50B GLN* 5.6 0.2 - - - +
149B LEU* 4.5 12.6 - - - +
153B VAL* 3.6 35.0 - - + +
157B ARG* 5.0 4.5 - - - -
223D C 5.2 2.0 + - - -
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Residues in contact with ALA 44 (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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40B VAL* 2.6 23.0 + - + +
41B ILE 3.9 3.4 - - - +
43B GLN* 1.3 72.8 - - - +
45B GLY* 1.3 59.7 + - - +
46B PHE* 3.6 8.1 - - + -
153B VAL* 3.9 10.3 - - + +
156B TYR* 3.6 30.3 - - + -
157B ARG* 3.6 29.7 - - - +
160B ASP* 3.7 15.4 - - - +
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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