Contacts of the helix formed by residues 37 - 57 (chain B) in PDB entry 4IYM
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 SER 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B THR* 3.0 24.1 + - - -
15B SER* 3.6 25.8 - - - -
35B LEU 3.4 1.6 + - - -
36B ALA* 1.3 79.2 - - - +
38B ASP* 1.3 64.7 + - - +
39B ALA* 3.3 6.6 + - - +
40B ASP* 3.1 16.7 + - - -
41B LEU* 3.2 20.1 + - - +
206B ALA* 5.9 1.1 - - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 1.3 72.9 - - - +
39B ALA* 1.3 60.1 + - - +
41B LEU* 3.4 5.4 + - - +
42B ALA* 2.8 32.5 + - - +
205B GLY 5.2 1.4 - - - +
209B ALA* 3.9 20.3 - - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 3.8 11.9 - - + +
37B SER* 3.3 10.1 + - - +
38B ASP* 1.3 77.3 - - - +
40B ASP* 1.3 53.5 + - - +
42B ALA* 3.3 6.1 + - - +
43B ALA* 2.8 37.0 + - - +
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Residues in contact with ASP 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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4B HIS* 2.8 40.8 + - + +
6B ILE* 3.5 15.5 - - + +
12B ALA 4.6 1.2 - - - +
13B GLY* 3.7 0.9 - - - -
14B THR* 2.7 38.7 + - - +
15B SER 4.2 0.3 + - - -
35B LEU 4.6 0.3 - - - +
36B ALA* 3.4 6.3 - - + -
37B SER* 3.1 32.6 + - - +
38B ASP 3.3 0.2 - - - -
39B ALA* 1.3 72.5 - - - +
41B LEU* 1.3 65.0 + - - +
43B ALA* 3.3 2.4 + - - -
44B ALA* 3.0 19.5 + - - +
200B VAL* 4.7 2.5 - - + -
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Residues in contact with LEU 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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36B ALA* 5.6 0.2 - - + -
37B SER 3.2 11.1 + - - +
38B ASP 4.0 4.7 - - - +
40B ASP* 1.3 76.9 - - - +
42B ALA* 1.3 57.3 + - - +
44B ALA* 3.1 5.5 + - - +
45B VAL* 2.9 28.5 + - + +
169B ILE* 4.2 28.5 - - + -
200B VAL* 4.4 14.4 - - + +
206B ALA* 5.3 2.2 - - + +
209B ALA* 3.4 47.1 - - + +
210B ILE* 3.7 26.9 - - + +
213B HIS* 3.9 21.8 - - + -
216B ILE* 4.3 2.2 - - + -
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Residues in contact with ALA 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 ASP 2.8 19.2 + - - +
39B ALA* 3.5 8.1 - - - +
41B LEU* 1.3 75.8 - - - +
43B ALA* 1.3 56.6 + - - +
45B VAL* 3.2 7.1 + - - +
46B GLU* 2.8 38.8 + - + +
213B HIS* 4.7 11.8 - - + +
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Residues in contact with ALA 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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6B ILE* 3.8 16.9 - - + +
39B ALA 2.8 20.5 + - - +
40B ASP* 3.7 5.8 - - - +
42B ALA* 1.3 72.8 - - - +
44B ALA* 1.3 58.2 + - - +
46B GLU* 3.9 6.1 - - - +
47B SER* 2.9 31.9 + - - -
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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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6B ILE* 4.0 11.3 - - + +
40B ASP 3.0 8.8 + - - +
41B LEU 3.1 8.5 + - - +
43B ALA* 1.3 76.3 - - - +
45B VAL* 1.3 58.5 + - - +
48B ALA* 2.9 26.2 + - - +
169B ILE* 4.1 9.9 - - + +
198B ASN* 3.0 29.3 + - + +
200B VAL* 3.5 31.6 - - + -
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Residues in contact with VAL 45 (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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41B LEU* 2.9 17.2 + - + +
42B ALA 3.6 6.3 - - - +
44B ALA* 1.3 73.3 - - - +
46B GLU* 1.3 65.4 + - - +
48B ALA* 3.2 4.6 + - - +
49B LYS* 2.8 45.1 + - + +
140B ILE* 4.6 4.3 - - + -
169B ILE* 3.5 23.6 - - + -
213B HIS* 3.3 39.3 - - + +
215B ASP* 3.9 8.5 - - + +
216B ILE* 4.0 20.9 - - + -
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Residues in contact with GLU 46 (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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42B ALA* 2.8 25.5 + - + +
43B ALA* 3.9 6.5 - - - +
45B VAL* 1.3 71.9 - - + +
47B SER* 1.3 61.7 + - - +
49B LYS* 2.9 41.5 + - - +
50B ALA* 3.0 29.8 + - - +
213B HIS* 5.8 0.3 + - - -
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Residues in contact with SER 47 (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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6B ILE* 4.0 9.9 - - - -
7B ASP* 3.3 23.4 + - - +
43B ALA 2.9 20.3 + - - -
46B GLU* 1.3 76.8 - - - +
48B ALA* 1.3 61.4 + - - +
50B ALA* 3.4 7.1 + - - +
51B ALA* 3.3 22.7 + - - +
195B GLY* 3.1 15.5 - - - -
198B ASN* 3.1 21.4 + - - -
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Residues in contact with ALA 48 (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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44B ALA 2.9 19.1 + - - +
45B VAL* 3.2 6.0 + - - +
47B SER* 1.3 76.8 + - - +
49B LYS* 1.3 57.0 + - - +
51B ALA* 3.2 0.7 + - - -
52B GLN* 2.9 34.0 + - - +
140B ILE* 4.0 21.1 - - + -
167B ALA* 3.7 20.7 - - + +
168B PHE 5.3 0.7 - - - +
169B ILE* 4.8 5.2 - - + -
195B GLY 3.3 15.2 + - - +
198B ASN* 4.4 1.8 - - - +
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Residues in contact with LYS 49 (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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45B VAL* 2.8 26.1 + - + +
46B GLU* 2.9 37.9 + - - +
48B ALA* 1.3 72.4 - - - +
50B ALA* 1.3 63.5 + - - +
52B GLN* 5.1 1.8 - - - -
53B PRO* 3.2 22.2 - - - +
140B ILE* 3.6 19.7 - - + -
215B ASP* 2.8 36.1 + - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 6.2 0.2 - - - +
46B GLU 3.0 16.9 + - - +
47B SER* 3.8 7.0 - - - +
48B ALA 3.3 0.2 - - - -
49B LYS* 1.3 77.8 - - - +
51B ALA* 1.3 58.3 + - + +
53B PRO* 4.1 6.1 - - - +
54B LYS* 5.4 3.8 + - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 5.8 0.2 - - - +
47B SER 3.3 12.5 + - - +
48B ALA 3.2 1.8 + - - +
49B LYS 3.2 0.6 - - - -
50B ALA* 1.3 76.8 - - + +
52B GLN* 1.3 66.7 + - - +
53B PRO* 3.3 3.8 - - - -
54B LYS* 3.5 6.4 + - - +
55B TRP* 3.2 15.9 + - - +
193B PRO* 5.1 4.8 - - + +
194B ALA 3.2 26.9 - - - +
195B GLY 4.2 2.9 - - - -
196B ILE* 3.4 19.1 - - + +
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Residues in contact with GLN 52 (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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48B ALA 2.9 18.0 + - - +
49B LYS* 4.8 1.3 - - - +
51B ALA* 1.3 76.8 - - - +
53B PRO* 1.4 72.4 - - + +
55B TRP* 3.1 2.0 + - - +
56B ALA* 2.8 44.0 + - - +
137B PRO* 3.7 15.0 - - - +
139B GLY* 3.5 32.1 - - - +
140B ILE* 5.1 4.0 - - + -
165B GLY 3.1 20.6 + - - +
166B ASN 4.1 0.2 - - - -
167B ALA* 3.6 18.4 - - + +
196B ILE* 3.6 8.9 - - - +
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Residues in contact with PRO 53 (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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49B LYS 3.2 20.6 - - - +
50B ALA 4.1 4.9 - - - +
51B ALA 3.5 3.6 - - - -
52B GLN* 1.4 103.6 - - + +
54B LYS* 1.3 56.9 + - + +
56B ALA* 3.3 5.1 + - + +
57B ALA* 2.9 30.0 + - - +
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Residues in contact with LYS 54 (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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50B ALA 5.4 1.0 + - - +
51B ALA* 3.5 7.7 + - - +
52B GLN 3.5 0.4 - - - -
53B PRO* 1.3 80.1 - - + +
55B TRP* 1.3 60.3 + - - +
57B ALA* 3.4 9.1 + - - +
58B THR* 2.9 25.2 + - - -
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Residues in contact with TRP 55 (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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51B ALA 3.2 4.8 + - - +
52B GLN 3.1 5.4 + - - +
54B LYS* 1.3 77.0 - - - +
56B ALA* 1.3 57.1 + - - +
58B THR* 3.0 37.1 + - + -
62B ARG 5.4 0.2 - - - -
63B ARG* 3.6 49.0 - - + -
66B VAL* 3.9 18.4 - - + -
67B PHE* 4.9 2.9 - + - -
162B ILE* 2.8 50.5 + - + +
165B GLY* 3.8 13.8 - - - -
166B ASN 3.5 18.6 + - - -
191B GLY 5.1 0.2 - - - -
192B LEU* 3.7 10.1 - - + -
193B PRO* 3.6 35.4 - - + +
196B ILE* 3.6 30.7 - - + -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 2.8 39.6 + - - +
53B PRO* 3.8 4.7 - - + +
55B TRP* 1.3 72.9 - - - +
57B ALA* 1.3 59.0 + - - +
58B THR 3.2 7.4 + - - +
63B ARG* 3.9 8.3 + - - +
137B PRO* 3.8 15.5 - - + -
165B GLY* 3.6 15.7 + - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO 2.9 17.4 + - - +
54B LYS* 3.7 9.9 - - - +
55B TRP 3.2 0.4 - - - -
56B ALA* 1.3 75.4 - - - +
58B THR* 1.3 61.9 + - - +
59B ASN* 3.7 1.4 + - - -
127C PRO* 5.8 4.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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