Contacts of the helix formed by residues 35 - 44 (chain A) in PDB entry 2M8L
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 GLU 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LYS* 4.4 24.9 + - + +
33A SER* 2.9 19.2 - - - +
34A PRO* 1.3 79.8 - - + +
36A VAL* 1.3 64.5 + - - +
37A ILE 3.3 0.2 + - - -
38A PRO* 3.5 14.9 - - - +
39A MET* 3.5 29.2 + - + +
203B LYS* 4.2 21.9 + - - -
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Residues in contact with VAL 36 (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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23A TRP* 3.7 30.0 - - + -
26A VAL* 4.4 12.8 - - + +
27A VAL* 4.8 5.8 - - + -
30A LYS* 3.0 39.3 - - + +
31A ALA 3.9 8.3 - - - +
32A PHE* 4.7 1.1 - - - -
33A SER 3.0 16.4 + - - +
35A GLU* 1.3 77.9 - - - +
37A ILE* 1.3 56.0 + - + +
39A MET* 3.3 2.8 + - - +
40A PHE* 2.8 33.2 + - + +
138A LEU* 4.9 12.6 - - + -
142A VAL* 5.6 2.2 - - + -
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Residues in contact with ILE 37 (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 PRO* 3.2 9.3 + - + +
36A VAL* 1.3 79.6 - - + +
38A PRO* 1.3 74.3 - - + +
40A PHE* 3.2 8.3 + - - +
41A SER* 3.0 22.8 + - - -
135A ILE* 4.2 27.5 - - + +
138A LEU* 3.7 25.1 - - + +
139A ASN* 3.5 43.1 - - + +
142A VAL* 4.8 11.9 - - + -
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Residues in contact with PRO 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 PRO 3.0 20.9 - - - +
35A GLU* 3.5 17.9 - - - +
37A ILE* 1.3 94.4 - - + +
39A MET* 1.3 61.6 + - + +
41A SER* 3.3 7.8 + - - -
42A ALA* 3.1 22.9 + - - +
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Residues in contact with MET 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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26A VAL* 4.0 36.1 - - + -
30A LYS* 4.7 17.3 - - - +
35A GLU* 3.5 18.1 + - + +
36A VAL 3.3 8.0 + - - +
37A ILE 3.2 0.6 - - - -
38A PRO* 1.3 77.9 - - + +
40A PHE* 1.3 67.4 + - - +
42A ALA* 3.1 8.6 + - - +
43A LEU* 2.9 38.2 + - + +
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Residues in contact with PHE 40 (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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23A TRP* 3.3 48.4 - + + -
36A VAL 2.8 20.9 + - - +
37A ILE 3.5 5.2 - - - +
39A MET* 1.3 73.3 - - - +
41A SER* 1.3 58.7 + - - +
43A LEU* 3.9 1.6 - - - +
44A SER* 3.0 54.5 + - - -
52A LEU* 4.0 18.6 - - + -
55A MET* 4.4 7.9 - - + -
56A LEU* 4.1 17.3 - - + -
131A LYS* 4.5 9.6 - - + -
134A ILE* 3.4 33.7 - - + -
135A ILE* 4.2 11.9 - - + -
138A LEU* 3.7 20.9 - - + -
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Residues in contact with SER 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 ILE* 3.0 13.3 + - - -
38A PRO* 3.6 11.0 - - - -
40A PHE* 1.3 83.1 - - - +
42A ALA* 1.3 62.4 + - - +
44A SER 3.5 6.8 + - - -
45A GLU* 3.6 11.1 + - - +
131A LYS* 4.2 22.1 + - - -
135A ILE* 4.4 16.6 - - - +
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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 PRO 3.1 13.8 + - - +
39A MET* 3.6 13.5 - - - +
41A SER* 1.3 78.1 - - - +
43A LEU* 1.3 66.7 + - + +
44A SER 3.4 0.3 + - - -
45A GLU* 3.5 21.9 + - - +
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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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15A ILE* 5.5 4.3 - - - +
19A THR* 3.6 33.8 - - + +
22A ALA* 4.2 14.6 - - + -
23A TRP* 3.6 45.1 - - + +
26A VAL* 4.2 12.1 - - + -
39A MET* 2.9 26.4 + - + +
40A PHE* 4.0 3.4 - - + +
42A ALA* 1.3 82.0 - - + +
44A SER* 1.3 57.8 + - - +
45A GLU 3.3 4.8 + - - +
55A MET* 4.4 10.9 - - + +
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Residues in contact with SER 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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15A ILE* 6.1 1.3 - - - -
40A PHE* 3.0 42.8 + - - -
41A SER 3.9 2.2 - - - -
42A ALA 3.3 0.4 - - - -
43A LEU* 1.3 75.3 - - - +
45A GLU* 1.3 65.6 + - - +
46A GLY 3.3 0.5 + - - -
47A ALA* 3.1 23.2 + - - +
52A LEU* 3.7 21.8 - - - +
55A MET* 4.5 10.8 - - - +
131A LYS* 4.2 19.6 + - - +
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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