Contacts of the helix formed by residues 32 - 45 (chain X) in PDB entry 1M6E
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 32 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28X VAL* 3.1 17.9 + - - +
29X ILE* 3.2 22.4 - - + +
30X SER 3.1 1.0 - - - -
31X ILE* 1.3 75.8 - - - +
33X LYS* 1.3 55.2 + - - +
34X PRO* 3.5 1.3 - - - -
35X ILE* 3.6 12.9 + - - +
36X THR* 2.6 38.2 + - - +
144X HIS* 4.6 13.9 - - + +
146X SER* 4.8 0.4 - - - +
206X VAL* 5.0 3.5 - - + +
208X THR* 3.6 23.2 + - - +
351X ILE* 3.8 24.5 - - - +
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Residues in contact with LYS 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ILE 3.6 6.6 + - - +
30X SER* 3.1 18.3 + - - +
32X THR* 1.3 77.1 - - - +
34X PRO* 1.4 64.5 - - + +
36X THR* 3.0 8.4 + - - -
37X GLU* 2.8 53.3 + - + +
72X GLU* 3.5 41.9 + - + -
76X THR* 5.0 2.1 + - - -
999X LU 3.7 20.2 - - - -
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Residues in contact with PRO 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X SER 4.3 0.7 - - - +
31X ILE 3.3 17.5 - - - +
32X THR 3.6 0.9 - - - -
33X LYS* 1.4 95.9 - - + +
35X ILE* 1.3 67.7 + - + +
37X GLU* 3.0 20.7 + - + +
38X ALA* 3.1 14.4 + - - +
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Residues in contact with ILE 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ILE 3.9 8.1 - - - +
32X THR* 3.7 31.2 - - - +
34X PRO* 1.3 80.1 - - + +
36X THR* 1.3 58.2 + - - +
38X ALA* 3.7 6.5 - - - +
39X ALA* 3.2 23.4 + - - +
206X VAL* 4.4 5.6 - - + -
276X HIS* 3.4 41.7 - - + +
278X GLU* 5.2 6.7 - - - +
351X ILE* 4.4 25.6 - - + -
353X SER* 3.7 28.9 + - - +
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Residues in contact with THR 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X THR* 2.6 31.9 + - - +
33X LYS* 3.0 8.6 + - - -
35X ILE* 1.3 75.9 - - - +
37X GLU* 1.3 62.9 + - - +
38X ALA 3.3 0.2 - - - -
39X ALA* 3.3 5.7 - - - +
40X ILE* 2.9 29.5 + - - +
69X ALA* 6.4 0.9 - - + -
73X LEU* 3.3 27.6 - - + -
142X PHE* 3.4 22.2 - - + -
144X HIS* 4.8 8.7 - - + -
206X VAL* 4.0 14.3 - - + +
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Residues in contact with GLU 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X LYS* 2.8 49.8 + - + +
34X PRO* 3.0 11.9 + - + +
36X THR* 1.3 80.1 - - - +
38X ALA* 1.3 64.5 + - - +
40X ILE* 3.3 0.9 + - - +
41X THR* 2.4 38.2 + - - +
72X GLU 3.7 11.6 - - - +
73X LEU* 4.7 2.1 - - - +
76X THR* 2.4 41.7 + - - +
999X LU 4.1 11.3 - - - -
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Residues in contact with ALA 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X PRO 3.1 7.8 + - - +
35X ILE* 3.7 11.2 - - - +
37X GLU* 1.3 77.0 - - - +
39X ALA* 1.3 57.3 + - - +
41X THR* 3.6 4.4 - - - -
42X ALA* 2.8 39.3 + - - +
204X ARG* 4.6 4.9 - - - +
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Residues in contact with ALA 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X ILE 3.2 13.7 + - - +
36X THR 3.3 9.6 - - - +
38X ALA* 1.3 81.0 - - - +
40X ILE* 1.3 58.7 + - - +
42X ALA* 3.7 1.4 - - - +
43X LEU* 3.2 25.8 + - - +
142X PHE* 3.8 8.5 - - + -
204X ARG* 3.5 25.5 - - + +
206X VAL* 3.7 24.9 - - + -
353X SER* 4.0 7.4 - - - +
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Residues in contact with ILE 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36X THR 2.9 16.2 + - - +
37X GLU* 4.5 1.1 - - - +
39X ALA* 1.3 71.5 - - - +
41X THR* 1.3 61.4 + - - +
43X LEU* 3.7 19.3 - - + -
44X TYR* 2.8 28.7 + - + +
53X LEU* 5.0 2.5 - - + -
55X ILE* 4.4 5.4 - - + -
73X LEU* 3.1 53.8 - - + +
76X THR* 5.0 8.1 - - + -
77X VAL* 3.4 27.1 - - + -
80X LEU* 4.4 1.5 - - - +
142X PHE* 3.2 23.8 - - + -
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Residues in contact with THR 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X GLU* 2.4 29.4 + - - +
38X ALA* 3.6 4.7 - - - -
40X ILE* 1.3 75.7 - - - +
42X ALA* 1.3 59.4 + - - +
44X TYR* 3.0 1.0 + - - +
45X SER* 2.7 47.4 + - - +
76X THR* 4.6 6.4 - - - +
80X LEU* 4.0 31.2 - - + +
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Residues in contact with ALA 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ALA 2.8 18.6 + - - +
39X ALA 3.7 4.7 - - - +
41X THR* 1.3 79.9 - - - +
43X LEU* 1.3 60.5 + - - +
45X SER* 3.5 21.8 - - - +
204X ARG* 3.9 22.7 - - - +
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Residues in contact with LEU 43 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X ALA 3.2 16.2 + - - +
40X ILE* 4.0 15.0 - - + +
42X ALA* 1.3 77.7 - - - +
44X TYR* 1.3 66.3 + - - +
45X SER 4.4 0.2 - - - +
46X GLY 3.8 3.1 - - - +
48X THR* 3.5 22.2 + - - +
49X VAL* 3.4 34.9 - - + +
53X LEU* 3.9 17.7 - - + -
141X HIS* 4.4 11.2 - - + -
142X PHE* 4.8 8.3 - - + -
200X VAL* 5.9 0.4 - - + -
202X GLY* 4.4 19.3 - - - +
203X GLY 4.7 0.7 - - - +
204X ARG* 3.7 23.5 - - + +
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Residues in contact with TYR 44 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ILE* 2.8 27.8 + - + +
41X THR 3.8 1.6 - - - +
43X LEU* 1.3 74.6 - - + +
45X SER* 1.3 53.7 + - - +
46X GLY 2.8 25.5 + - - +
47X ASP* 4.9 0.2 - - - -
49X VAL* 4.1 27.4 - - + +
50X THR 5.5 0.7 - - - -
53X LEU* 6.0 0.2 - - + -
77X VAL* 3.8 24.2 - - + -
80X LEU* 3.4 29.2 - - + -
81X ARG* 3.0 39.9 - - + +
85X GLY* 5.1 5.6 - - - -
86X ARG* 2.7 50.2 + - + +
88X ASN 4.1 2.9 + - - -
90X PRO* 4.2 9.8 - - + +
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Residues in contact with SER 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41X THR* 2.7 34.6 + - - +
42X ALA* 3.5 16.9 - - - +
43X LEU 4.4 0.3 - - - +
44X TYR* 1.3 69.0 - - - +
46X GLY* 1.3 65.9 + - - +
80X LEU* 5.5 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