Contacts of the helix formed by residues 36 - 46 (chain A) in PDB entry 5MS0
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY 3.6 2.4 - - - -
35A PHE* 1.3 79.2 - - - +
37A HIS* 1.3 61.1 + - - +
38A THR 3.4 1.8 - - - -
39A LEU* 3.3 7.4 + - - +
40A GLY* 3.1 23.6 + - - -
185A TYR* 5.4 5.8 - - - +
187A VAL* 5.2 14.6 - - - -
199A ASP* 5.4 3.9 - - - +
201A LEU* 4.8 12.4 - - - +
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Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 5.2 1.0 + - - -
36A GLY* 1.3 73.0 - - - +
38A THR* 1.3 61.3 + - - +
40A GLY* 3.9 1.1 - - - +
41A ASN* 3.0 32.1 + - - +
1217C THR 5.1 0.4 - - - -
1218C GLY* 3.2 35.0 - - - +
1219C GLU* 3.9 10.5 - - - -
1220C GLN 5.1 0.7 - - - +
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY 5.1 10.3 + - - -
35A PHE* 5.7 2.7 - - - -
36A GLY 3.4 1.2 - - - +
37A HIS* 1.3 77.2 - - - +
39A LEU* 1.3 58.4 + - - +
41A ASN* 4.6 3.4 - - - +
42A ALA* 3.0 33.8 + - - +
42B ALA* 5.4 13.5 - - - -
45B ARG* 5.8 7.9 - - - -
1217C THR 5.1 4.7 - - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE 4.4 11.5 + - - +
36A GLY* 3.3 12.6 + - - +
37A HIS 3.2 0.2 - - - -
38A THR* 1.3 74.6 - - - +
40A GLY* 1.3 66.6 + - - +
42A ALA* 4.3 1.4 - - - +
43A LEU* 3.1 26.9 + - - +
201A LEU* 5.4 6.1 - - + -
227B GLN* 5.3 9.6 - - + +
228B LEU* 5.7 8.3 - - - +
230B ALA* 4.6 19.7 - - + -
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY 3.1 10.5 + - - -
37A HIS* 3.6 2.4 + - - -
39A LEU* 1.3 79.6 - - - +
41A ASN* 1.3 58.1 + - - +
43A LEU* 3.8 1.9 - - - -
44A ARG* 3.0 27.5 + - - +
183A ILE* 6.1 1.2 - - - +
185A TYR* 5.0 15.0 - - - +
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS 3.0 18.9 + - - +
38A THR* 4.5 1.8 - - - +
40A GLY* 1.3 76.0 - - - +
42A ALA* 1.3 62.0 + - - +
44A ARG* 3.7 6.2 - - - +
45A ARG* 2.9 26.0 + - - +
1214C ASP 4.6 6.5 - - - +
1215C GLY* 4.8 9.9 - - - +
1216C ARG 4.6 7.0 - - - +
1217C THR 4.0 20.0 - - - +
1218C GLY* 4.2 8.7 - - - -
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR 3.0 21.2 + - - +
39A LEU* 4.3 1.6 - - - +
41A ASN* 1.3 78.4 - - - +
43A LEU* 1.3 56.7 + - - +
44A ARG 3.2 0.2 - - - -
45A ARG* 3.2 9.1 + - - +
46A ILE* 3.0 26.7 + - - +
228B LEU* 5.3 12.3 - - + -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU 3.1 15.9 + - - +
40A GLY* 3.8 2.9 - - - +
42A ALA* 1.3 75.2 - - - +
44A ARG* 1.3 58.1 + - - +
46A ILE* 4.1 10.3 - - + +
47A LEU* 3.3 24.3 - - + +
183A ILE* 5.7 4.3 - - - +
228B LEU* 5.5 12.5 - - + +
231B PHE* 4.8 18.4 - - + -
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 3.0 20.7 + - - +
41A ASN* 3.8 7.9 - - - +
42A ALA 3.2 0.2 - - - -
43A LEU* 1.3 76.1 - - - +
45A ARG* 1.3 64.7 + - - +
46A ILE 3.4 0.2 - - - -
47A LEU* 3.9 4.0 + - - +
48A LEU* 3.9 19.8 + - - +
183A ILE* 6.2 4.5 - - + -
1215C GLY* 5.6 5.2 - - - +
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Residues in contact with ARG 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN 2.9 15.0 + - - +
42A ALA* 3.3 13.5 - - - +
44A ARG* 1.3 80.1 - - - +
46A ILE* 1.3 61.6 + - - +
48A LEU* 4.4 4.5 + - - +
49A SER* 5.0 3.6 + - - -
50A SER* 5.8 0.2 - - - -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 3.0 14.9 + - - +
43A LEU* 4.5 6.3 - - + -
45A ARG* 1.3 78.4 - - - +
47A LEU* 1.3 58.4 + - + +
48A LEU 2.9 9.2 + - - -
50A SER* 3.3 36.0 + - - -
220A ALA* 5.2 15.5 - - + +
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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