Contacts of the helix formed by residues 25 - 44 (chain A) in PDB entry 1M1I
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 ALA 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ARG* 3.8 37.0 - - - +
24A GLU* 1.3 79.8 - - - +
26A VAL* 1.3 60.7 + - - +
27A ILE* 3.4 8.3 - - - +
28A ALA* 3.2 13.2 + - - +
29A GLN* 2.8 38.4 + - + +
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Residues in contact with VAL 26 (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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12A THR* 3.5 29.8 - - + +
16A PHE* 4.5 11.2 - - + +
17A PHE* 3.6 37.0 - - + +
24A GLU* 3.9 11.6 + - + +
25A ALA* 1.3 84.2 - - - +
27A ILE* 1.3 70.8 + - + +
29A GLN* 3.3 4.7 + - - +
30A ILE* 2.9 25.0 + - - +
61A ILE* 3.5 31.4 - - + -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 5.2 1.8 - - + -
25A ALA 4.4 12.1 - - - +
26A VAL* 1.3 80.4 - - + +
28A ALA* 1.3 67.3 + - + +
30A ILE* 3.2 11.1 - - - +
31A SER* 2.9 31.8 + - - -
59A ILE* 3.1 37.9 - - + -
61A ILE* 3.9 17.0 - - + -
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Residues in contact with ALA 28 (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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24A GLU 5.5 0.9 - - - +
25A ALA* 3.2 16.7 + - - +
27A ILE* 1.3 82.4 - - + +
29A GLN* 1.3 65.5 + - - +
31A SER* 2.7 22.7 + - - -
32A SER* 3.0 17.5 + - - +
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Residues in contact with GLN 29 (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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16A PHE* 3.7 25.3 - - + -
25A ALA* 2.8 18.9 + - + +
26A VAL* 3.6 4.9 - - - +
28A ALA* 1.3 76.0 - - - +
30A ILE* 1.3 65.9 + - + +
32A SER* 3.8 5.2 - - - -
33A HIS* 2.9 34.1 + - - +
102A PHE* 5.9 1.6 - - - -
149A VAL* 5.6 5.3 - - - +
158A PRO* 5.6 6.9 - - - +
161A SER* 4.5 16.6 + - - -
162A HIS* 5.9 2.2 + - - -
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Residues in contact with ILE 30 (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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10A ILE* 3.4 25.1 - - + -
12A THR* 3.6 27.8 - - + -
16A PHE* 4.0 13.9 - - + -
26A VAL 2.9 17.9 + - - +
27A ILE* 3.2 11.7 - - - +
29A GLN* 1.3 83.3 - - - +
31A SER* 1.3 60.2 + - - +
33A HIS* 3.0 5.0 + - - +
34A VAL* 2.8 56.1 + - + +
56A VAL* 5.2 1.3 - - + -
59A ILE* 3.1 31.9 - - + -
102A PHE* 5.2 7.9 - - + -
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Residues in contact with SER 31 (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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27A ILE* 2.9 24.2 + - - +
28A ALA* 2.7 24.9 + - - -
30A ILE* 1.3 82.8 - - - +
32A SER* 1.3 60.3 + - - +
34A VAL* 2.8 28.4 - - - +
35A LYS* 3.2 11.8 + - - +
56A VAL* 5.5 5.4 - - - -
59A ILE* 4.9 2.0 - - - -
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Residues in contact with SER 32 (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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28A ALA* 3.0 17.1 + - - +
29A GLN* 3.8 4.7 - - - -
31A SER* 1.3 80.9 + - - +
33A HIS* 1.3 64.8 + - - +
35A LYS* 3.4 9.1 + - - +
36A ALA* 2.9 24.5 + - - +
162A HIS* 4.4 2.9 - - - -
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Residues in contact with HIS 33 (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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29A GLN* 2.9 28.8 + - - +
30A ILE* 3.3 9.2 - - - +
32A SER* 1.3 74.7 - - - +
34A VAL* 1.3 56.4 + - - +
36A ALA* 2.9 6.9 + - - +
37A ILE* 2.8 47.8 + - + +
102A PHE* 4.1 21.9 - + - -
147A ILE* 4.6 1.6 - - + -
149A VAL* 6.2 0.4 - - + -
161A SER* 2.9 48.6 + - - -
162A HIS* 3.6 19.3 + - + -
165A PHE* 2.8 33.0 - + + +
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Residues in contact with VAL 34 (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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8A LEU* 5.1 0.4 - - + -
10A ILE* 4.6 10.5 - - + -
30A ILE* 2.8 39.6 + - + +
31A SER* 2.8 34.3 - - - +
33A HIS* 1.3 76.6 - - + +
35A LYS* 1.3 55.6 + - + +
37A ILE* 3.0 12.9 - - - +
38A ASP 2.8 30.0 + - - -
54A PHE* 2.8 40.5 - - + -
56A VAL* 4.4 16.4 - - + -
102A PHE* 5.0 9.9 - - + -
165A PHE* 5.2 0.9 - - + -
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Residues in contact with LYS 35 (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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31A SER 3.2 15.0 + - - +
32A SER* 3.6 8.5 - - - +
34A VAL* 1.3 81.8 - - + +
36A ALA* 1.3 58.5 + - - +
38A ASP* 3.1 11.6 + - + +
39A THR* 3.0 41.7 + - + +
54A PHE* 4.4 1.6 - - - -
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Residues in contact with ALA 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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32A SER 2.9 11.9 + - - +
33A HIS 2.9 10.2 + - - +
35A LYS* 1.3 74.7 - - - +
37A ILE* 1.3 62.0 + - - +
39A THR* 2.5 30.5 + - - -
40A ILE* 3.6 9.4 + - - +
162A HIS* 3.3 27.8 - - + +
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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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33A HIS* 2.8 42.6 - - + +
34A VAL* 3.0 13.7 + - - +
36A ALA* 1.3 76.1 - - - +
38A ASP* 1.3 62.6 + - - +
40A ILE* 3.0 24.6 + - - +
41A TYR* 3.1 48.2 + - + -
54A PHE* 3.5 20.0 - - + -
162A HIS* 4.6 9.6 - - - +
165A PHE* 3.2 37.7 - - + -
166A ALA* 5.0 4.7 - - + +
169A VAL* 4.2 1.8 - - + -
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Residues in contact with ASP 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 VAL 2.8 13.7 + - - +
35A LYS* 3.1 15.0 + - - +
37A ILE* 1.3 77.3 - - - +
39A THR* 1.3 56.3 + - - +
41A TYR* 3.3 2.2 + - - +
42A GLN* 2.7 40.6 + - - +
53A SER* 2.7 36.3 + - - -
54A PHE* 3.1 30.9 + - + +
55A MET* 4.7 13.1 - - - +
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Residues in contact with THR 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 LYS* 3.0 33.3 + - + +
36A ALA* 2.5 22.9 + - - +
38A ASP* 1.3 77.2 - - - +
40A ILE* 1.3 56.5 + - - +
42A GLN* 4.2 3.5 - - - -
43A THR* 2.8 43.8 + - - +
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Residues in contact with ILE 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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36A ALA 3.8 14.1 - - - +
37A ILE* 3.0 10.9 + - - +
39A THR* 1.3 83.1 + - - +
41A TYR* 1.3 58.9 + - + +
43A THR* 2.9 17.3 + - - -
44A THR* 2.8 26.0 - - + +
162A HIS* 5.5 8.7 - - + +
163A ILE* 6.2 0.7 - - - -
166A ALA* 4.6 17.3 - - + -
200A ILE* 4.5 1.3 - - + -
214A ASN* 3.0 52.3 - - + +
215A LYS* 4.9 2.7 - - + -
216A PHE* 4.2 22.9 - - + -
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Residues in contact with TYR 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* 3.1 30.6 + - + +
38A ASP* 3.8 4.9 - - - +
40A ILE* 1.3 78.2 - - + +
42A GLN* 1.3 63.0 + - - +
43A THR 3.1 1.0 + - - -
44A THR* 3.1 21.8 + - - +
46A PHE* 3.5 13.9 - + - -
52A ILE* 3.1 17.2 - - + +
53A SER* 3.7 15.9 - - - +
54A PHE* 5.5 0.7 - - + -
166A ALA* 2.8 20.3 + - + -
169A VAL* 2.8 37.9 - - + +
170A GLY* 2.9 14.6 + - - -
173A PHE* 4.0 43.7 - + + -
216A PHE* 3.2 25.6 - + - -
224A ILE* 5.2 1.3 - - + -
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Residues in contact with GLN 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 ASP* 2.7 26.3 + - - +
39A THR* 4.2 4.0 - - - +
41A TYR* 1.3 71.6 - - - +
43A THR* 1.3 71.2 + - + +
44A THR 3.7 0.2 + - - -
50A ARG* 4.2 2.9 - - - +
51A ASN* 2.7 66.8 + - - +
52A ILE 3.2 4.0 - - - -
53A SER* 2.8 23.5 + - - +
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Residues in contact with THR 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 THR* 2.8 31.0 + - - +
40A ILE* 2.9 14.0 + - - -
42A GLN* 1.3 88.1 - - + +
44A THR* 1.3 62.6 + - - +
45A ASP* 3.6 3.3 + - - +
50A ARG* 4.9 6.9 - - - +
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Residues in contact with THR 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 ILE* 2.8 33.3 + - + +
41A TYR* 3.1 10.4 + - - +
43A THR* 1.3 79.4 - - - +
45A ASP* 1.3 63.3 + - - +
46A PHE* 2.8 62.9 + - + -
50A ARG* 3.7 13.6 - - - +
52A ILE* 5.1 0.2 - - - +
215A LYS* 6.3 2.5 - - - -
216A PHE* 4.0 14.8 - - + +
221A ILE* 4.6 5.7 - - - +
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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