Contacts of the helix formed by residues 37 - 57 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.8 5.4 + - - -
15A SER* 3.8 19.1 - - - -
17A ARG* 6.5 0.2 - - - +
35A LEU 3.4 2.8 + - - -
36A ALA* 1.3 76.1 - - - +
38A ASP* 1.3 66.0 + - - +
39A ALA* 3.5 10.2 + - - +
40A ASP* 3.1 31.3 + - - +
41A LEU* 3.1 19.8 + - - +
206A ALA* 5.7 1.4 - - - -
209A ALA* 5.5 0.9 - - - -
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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
----------------------------------------------------------
37A SER* 1.3 74.5 - - - +
39A ALA* 1.3 57.2 + - - +
41A LEU* 3.4 3.6 + - - +
42A ALA* 2.9 28.1 + - - +
205A GLY* 4.2 8.8 - - - +
209A ALA* 3.7 28.0 - - + +
213A HIS* 5.9 0.3 - - - -
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Residues in contact with ALA 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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14A THR* 4.7 7.6 - - - +
37A SER* 3.2 9.4 + - - +
38A ASP* 1.3 76.4 - - - +
40A ASP* 1.3 65.8 + - - +
42A ALA* 3.4 7.6 + - - +
43A ALA* 3.0 23.6 + - - +
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Residues in contact with ASP 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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4A HIS* 4.1 8.3 + - + +
6A ILE* 4.0 9.0 - - + +
13A GLY* 3.6 11.3 - - - -
14A THR* 2.7 45.1 + - - +
15A SER* 3.6 5.4 + - - -
36A ALA* 3.7 18.1 - - + -
37A SER* 3.1 32.9 + - - +
39A ALA* 1.3 77.0 - - - +
41A LEU* 1.3 59.4 + - - +
43A ALA* 3.5 7.5 + - - +
44A ALA* 3.2 20.4 + - - +
200A VAL* 4.9 2.0 - - + +
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Residues in contact with LEU 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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36A ALA* 4.6 1.7 - - + +
37A SER 3.1 12.0 + - - +
38A ASP 3.7 8.1 - - - +
39A ALA 3.3 0.2 - - - -
40A ASP* 1.3 73.5 - - - +
42A ALA* 1.3 64.3 + - - +
44A ALA* 3.1 5.7 + - - +
45A VAL* 3.0 27.9 + - + -
169A ILE* 4.0 23.3 - - + -
200A VAL* 4.1 19.7 - - + -
206A ALA* 4.6 3.6 - - - +
209A ALA* 3.9 31.2 - - + +
210A ILE* 3.7 28.5 - - + +
213A HIS* 3.8 25.8 - - + -
216A ILE* 4.5 0.4 - - + -
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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 ASP 2.9 17.1 + - - +
39A ALA* 3.6 9.4 - - - +
41A LEU* 1.3 75.3 - - - +
43A ALA* 1.3 57.4 + - - +
45A VAL* 3.2 1.9 + - - +
46A GLU* 2.8 38.6 + - + +
213A HIS* 4.2 20.4 - - + +
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Residues in contact with ALA 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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6A ILE* 4.3 10.6 - - + +
39A ALA 3.0 13.1 + - - +
40A ASP* 3.6 11.7 - - - +
41A LEU 3.2 0.2 - - - -
42A ALA* 1.3 74.6 - - - +
44A ALA* 1.3 58.1 + - - +
46A GLU* 3.4 7.3 + - - +
47A SER* 3.0 29.3 + - - -
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Residues in contact with ALA 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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6A ILE* 3.8 16.7 - - + +
40A ASP 3.2 3.5 + - - +
41A LEU 3.1 8.8 + - - +
43A ALA* 1.3 78.9 - - - +
45A VAL* 1.3 57.6 + - - +
47A SER 3.4 0.5 + - - -
48A ALA* 3.0 25.8 + - - +
169A ILE* 4.3 8.6 - - + +
198A ASN* 3.1 25.7 + - + +
200A VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 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 LEU* 3.0 34.1 + - + +
42A ALA 3.7 6.5 - - - +
44A ALA* 1.3 72.3 - - - +
46A GLU* 1.3 61.8 + - - +
48A ALA* 3.2 4.1 + - - +
49A LYS* 2.8 34.2 + - + +
140A ILE* 4.1 7.4 - - + +
169A ILE* 3.4 25.8 - - + -
213A HIS* 3.4 33.9 - - + +
215A ASP* 3.8 17.3 - - + -
216A ILE* 3.9 11.4 - - + -
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Residues in contact with GLU 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* 2.8 23.8 + - + +
43A ALA* 3.9 6.7 - - - +
45A VAL* 1.3 79.5 - - - +
47A SER* 1.3 57.6 + - - +
49A LYS* 2.7 44.5 + - - +
50A ALA* 3.0 29.6 + - - +
213A HIS* 4.8 3.8 + - - -
215A ASP* 4.1 2.8 - - - +
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Residues in contact with SER 47 (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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6A ILE* 4.0 7.4 - - - -
7A ASP* 2.5 35.5 + - - +
43A ALA 3.0 16.5 + - - -
44A ALA 3.6 4.0 - - - -
45A VAL 3.2 0.2 - - - -
46A GLU* 1.3 75.1 - - - +
48A ALA* 1.3 62.8 + - - +
50A ALA* 3.4 6.1 + - - +
51A ALA* 3.2 24.6 + - - +
195A GLY* 3.2 6.7 - - - -
198A ASN* 3.1 17.9 + - - -
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Residues in contact with ALA 48 (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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44A ALA 3.0 17.5 + - - +
45A VAL* 3.2 5.8 + - - +
47A SER* 1.3 74.8 + - - +
49A LYS* 1.3 58.6 + - - +
52A GLN* 2.9 35.5 + - - +
140A ILE* 4.1 20.0 - - + -
167A ALA* 3.6 21.7 - - + +
168A PHE 5.0 0.7 - - - +
169A ILE* 4.7 6.5 - - + -
195A GLY 3.3 14.8 + - - +
198A ASN* 4.4 2.2 - - - +
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Residues in contact with LYS 49 (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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45A VAL* 2.8 21.2 + - + +
46A GLU* 2.7 43.8 + - - +
48A ALA* 1.3 71.8 - - - +
50A ALA* 1.3 61.2 + - - +
52A GLN* 5.1 1.1 - - - -
53A PRO* 3.4 20.6 - - - +
140A ILE* 3.5 19.0 - - + +
215A ASP* 3.0 34.0 + - + +
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Residues in contact with ALA 50 (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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46A GLU 3.0 16.3 + - - +
47A SER* 3.9 6.7 - - - +
48A ALA 3.3 0.2 - - - -
49A LYS* 1.3 77.5 - - - +
51A ALA* 1.3 59.9 + - - +
53A PRO* 4.2 5.4 - - - +
54A LYS* 5.5 2.6 + - - +
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Residues in contact with ALA 51 (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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7A ASP* 5.6 0.7 - - - +
47A SER 3.2 16.1 + - - +
48A ALA 4.2 0.4 - - - +
50A ALA* 1.3 78.9 - - - +
52A GLN* 1.3 65.9 + - - +
53A PRO 3.4 2.0 - - - -
54A LYS* 3.5 8.6 + - - +
55A TRP* 3.4 13.7 + - - +
193A PRO* 5.3 4.4 - - + +
194A ALA 3.2 27.6 - - - +
195A GLY 4.0 3.6 - - - -
196A ILE* 3.6 16.9 - - + +
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Residues in contact with GLN 52 (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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48A ALA 2.9 18.6 + - - +
49A LYS* 4.7 1.1 - - - +
51A ALA* 1.3 76.1 - - - +
53A PRO* 1.4 72.8 - - + +
55A TRP* 3.1 3.1 + - - +
56A ALA* 2.8 41.1 + - - +
137A PRO* 3.6 16.6 - - - +
139A GLY* 3.4 31.8 + - - +
140A ILE* 4.9 4.2 - - + +
165A GLY 2.9 21.3 + - - +
166A ASN 4.0 0.2 - - - -
167A ALA* 3.5 18.6 - - + +
196A ILE* 3.7 9.4 - - + +
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Residues in contact with PRO 53 (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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49A LYS 3.4 19.5 - - - +
50A ALA 4.2 5.6 - - - +
51A ALA 3.6 2.9 - - - -
52A GLN* 1.4 101.7 - - + +
54A LYS* 1.3 57.0 + - + +
56A ALA* 3.3 5.9 + - + +
57A ALA* 2.9 29.2 + - - +
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Residues in contact with LYS 54 (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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50A ALA 5.5 1.1 + - - +
51A ALA* 3.5 8.6 + - - +
52A GLN 3.4 0.6 - - - -
53A PRO* 1.3 78.9 - - + +
55A TRP* 1.3 60.3 + - - +
57A ALA* 3.3 9.1 + - + +
58A THR* 3.0 25.7 + - - -
193A PRO* 6.2 0.9 - - + -
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Residues in contact with TRP 55 (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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51A ALA 3.4 2.7 + - - +
52A GLN 3.1 3.9 + - - +
54A LYS* 1.3 79.0 - - - +
56A ALA* 1.3 60.2 + - - +
58A THR* 3.1 32.2 + - + -
62A ARG 5.3 0.4 - - - -
63A ARG* 3.5 49.7 - - + -
66A VAL* 3.7 23.3 - - + -
67A PHE* 4.9 2.5 - + - -
162A ILE* 2.8 48.7 + - + +
165A GLY* 3.6 14.7 - - - -
166A ASN 3.6 17.9 + - - -
191A GLY 5.1 0.2 - - - -
192A LEU* 3.8 6.5 - - + -
193A PRO* 3.5 37.4 - - + +
196A ILE* 3.5 31.0 - - + -
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Residues in contact with ALA 56 (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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52A GLN* 2.8 40.5 + - - +
53A PRO* 3.7 6.1 - - + +
55A TRP* 1.3 73.7 - - - +
57A ALA* 1.3 59.6 + - - +
58A THR 3.5 6.3 + - - +
63A ARG* 4.1 7.1 + - - +
137A PRO* 3.9 15.5 - - + +
165A GLY* 3.5 14.3 + - - +
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Residues in contact with ALA 57 (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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53A PRO 2.9 17.2 + - - +
54A LYS* 3.6 10.8 - - + +
55A TRP 3.2 0.6 - - - -
56A ALA* 1.3 76.0 - - - +
58A THR* 1.3 60.1 + - - +
59A ASN 3.8 2.3 + - - -
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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
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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