Contacts of the helix formed by residues 49 - 67 (chain A) in PDB entry 4IRX
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 GLN 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASN* 3.7 11.1 - - - +
46A ASP* 3.3 26.9 + - + +
47A LEU 3.2 1.0 - - - -
48A SER* 1.3 78.1 - - - +
50A PRO* 1.3 71.8 - - + +
51A PHE* 4.4 2.2 - - + +
52A PHE* 3.0 40.8 + - + +
53A VAL* 3.0 14.1 + - - +
77A ASN* 5.8 0.4 + - - -
169A ASP* 3.0 32.7 + - - -
202A ASN 5.1 0.8 + - - -
203A SER* 3.7 18.5 + - - +
204A LYS* 4.5 4.4 - - - +
231A ASN* 4.7 1.7 + - - +
401A INS 2.6 27.2 + - - +
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Residues in contact with PRO 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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48A SER 3.6 7.6 - - - +
49A GLN* 1.3 84.3 - - + +
51A PHE* 1.3 63.0 + - - +
53A VAL* 3.4 9.8 + - + +
54A ALA* 3.1 23.0 + - - +
57A ARG* 5.5 0.3 + - - -
205A ARG* 5.2 3.4 - - - +
231A ASN* 6.2 0.4 - - - +
233A ASP* 3.4 41.7 - - + +
260A ILE* 5.0 15.0 - - + -
321A ARG* 4.9 2.7 + - - -
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Residues in contact with PHE 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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49A GLN* 3.2 1.9 - - + +
50A PRO* 1.3 80.3 - - - +
52A PHE* 1.3 74.9 + + + +
54A ALA* 3.4 6.2 + - - +
55A MSE 3.0 38.8 + - + +
125A ASP* 3.5 19.7 - - - -
258A ASP* 3.5 28.3 - - + +
260A ILE* 4.9 11.0 - - + +
278A GLN* 3.3 34.3 - - + -
280A PRO* 3.5 38.2 - - + +
321A ARG* 5.2 2.0 - - - +
401A INS 3.3 34.5 - - - +
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Residues in contact with PHE 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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44A PHE* 3.8 23.6 - + + -
45A ASN* 3.5 29.8 - - - -
46A ASP 4.0 12.6 - - - +
47A LEU* 3.6 13.8 - - + +
49A GLN* 3.0 39.8 + - + +
51A PHE* 1.3 101.6 - + - +
53A VAL* 1.3 59.8 + - - +
54A ALA 3.2 1.3 - - - -
55A MSE 3.2 12.3 + - - +
56A ARG* 2.8 29.8 + - - +
100A ALA* 4.5 5.8 - - + -
125A ASP* 3.4 36.3 - - + -
126A ARG* 4.0 7.9 - - - -
401A INS 4.1 3.4 - - - -
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Residues in contact with VAL 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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47A LEU* 3.2 34.5 - - + +
48A SER* 4.8 1.8 - - - +
49A GLN 3.0 13.0 + - - +
50A PRO* 3.4 11.4 + - + +
52A PHE* 1.3 73.9 - - - +
54A ALA* 1.3 62.2 + - - +
56A ARG* 3.3 7.0 + - - +
57A ARG* 3.2 43.5 + - + +
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Residues in contact with ALA 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 PRO 3.1 10.0 + - - +
51A PHE 3.6 8.1 - - - +
53A VAL* 1.3 78.8 - - - +
55A MSE 1.3 61.9 + - - +
57A ARG* 3.2 29.8 + - - +
58A GLU* 3.4 18.6 + - - +
280A PRO* 6.3 2.2 - - + -
321A ARG* 3.5 45.1 - - - +
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Residues in contact with MSE 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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44A PHE* 4.1 18.2 - - + -
51A PHE* 3.0 32.6 + - + +
52A PHE* 3.2 20.2 + - - +
54A ALA* 1.3 76.4 - - - +
56A ARG* 1.3 62.5 + - - +
58A GLU* 3.1 11.4 + - - +
59A LEU* 3.0 19.4 + - - +
124A VAL* 4.3 14.1 - - + -
125A ASP* 4.3 6.7 - - + -
280A PRO* 3.7 41.0 - - + +
283A GLN* 4.1 18.8 - - + +
284A ILE* 3.6 30.5 - - + +
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Residues in contact with ARG 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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44A PHE* 4.1 18.1 - - + -
47A LEU* 3.6 29.8 - - + +
52A PHE 2.8 16.7 + - - +
53A VAL* 3.5 7.4 - - - +
54A ALA 3.2 0.2 - - - -
55A MSE 1.3 75.3 - - - +
57A ARG* 1.3 64.0 + - + +
59A LEU* 3.2 9.8 + - + +
60A GLU* 3.0 49.7 + - + +
72A VAL* 3.7 35.4 + - + +
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Residues in contact with ARG 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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50A PRO 5.5 0.2 + - - -
53A VAL* 3.2 29.2 + - + +
54A ALA* 3.2 25.7 + - - +
56A ARG* 1.3 79.5 - - + +
58A GLU* 1.3 68.4 + - - +
60A GLU* 3.4 14.6 + - - +
61A ASP* 3.2 20.6 + - - +
321A ARG* 3.6 25.3 - - - +
324A GLU* 4.2 7.9 + - - -
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Residues in contact with GLU 58 (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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54A ALA* 3.6 15.4 - - - +
55A MSE 3.1 7.5 + - - +
57A ARG* 1.3 79.6 + - - +
59A LEU* 1.3 66.1 + - - +
61A ASP* 3.3 3.8 + - - +
62A GLU* 3.0 25.2 + - - +
281A GLY* 3.8 29.6 - - - +
284A ILE* 4.1 5.2 - - + -
285A ARG* 2.7 40.6 + - - +
321A ARG* 5.9 3.6 + - - +
324A GLU* 5.1 6.6 - - - +
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Residues in contact with LEU 59 (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 VAL* 3.9 39.3 - - + -
44A PHE* 4.0 10.5 - - + -
55A MSE 3.0 12.4 + - - +
56A ARG* 3.2 11.2 + - + +
58A GLU* 1.3 77.9 - - - +
60A GLU* 1.3 58.0 + - + +
62A GLU* 3.4 3.7 + - - +
63A ALA* 2.9 28.2 + - - +
70A VAL* 4.2 11.4 - - + -
72A VAL* 3.9 22.0 - - + -
98A ILE* 5.2 0.4 - - + -
284A ILE* 3.7 32.0 - - + +
288A LEU* 4.0 24.9 - - + -
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Residues in contact with GLU 60 (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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56A ARG* 3.0 54.4 + - + +
57A ARG* 3.8 13.8 - - - +
58A GLU 3.3 0.2 - - - -
59A LEU* 1.3 77.5 - - + +
61A ASP* 1.3 63.2 + - - +
63A ALA* 3.4 6.7 + - - +
64A ALA* 3.1 22.9 + - - +
70A VAL* 4.9 11.0 - - + -
72A VAL* 5.3 2.5 - - + +
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Residues in contact with ASP 61 (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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57A ARG 3.2 11.3 + - - +
58A GLU* 3.7 6.7 - - - +
59A LEU 3.3 0.2 - - - -
60A GLU* 1.3 75.3 - - - +
62A GLU* 1.3 65.1 + - - +
64A ALA* 3.2 7.7 + - - +
65A LYS* 2.8 49.0 + - - +
285A ARG* 2.7 35.5 + - - +
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Residues in contact with GLU 62 (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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58A GLU 3.0 14.3 + - - +
59A LEU* 3.9 4.3 - - - +
61A ASP* 1.3 80.1 + - - +
63A ALA* 1.3 56.6 + - - +
65A LYS* 3.2 14.9 + - - +
66A LEU* 2.9 58.8 + - + +
285A ARG* 2.8 49.5 + - + +
288A LEU* 3.9 9.4 - - + -
289A ARG* 2.8 45.8 + - - +
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Residues in contact with ALA 63 (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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59A LEU 2.9 18.4 + - - +
60A GLU* 3.7 4.5 - - - +
61A ASP 3.2 0.2 - - - -
62A GLU* 1.3 77.1 - - - +
64A ALA* 1.3 61.5 + - - +
66A LEU 3.3 1.2 + - - -
67A GLY 3.1 3.6 + - - -
68A VAL* 3.0 45.1 + - - +
70A VAL* 3.8 32.3 - - + -
288A LEU* 3.6 10.0 - - + +
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Residues in contact with ALA 64 (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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60A GLU 3.1 13.6 + - - +
61A ASP* 3.5 10.1 - - - +
63A ALA* 1.3 75.4 - - - +
65A LYS* 1.3 63.5 + - + +
67A GLY* 3.0 15.0 + - - -
68A VAL 5.1 0.2 - - - -
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Residues in contact with LYS 65 (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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61A ASP* 2.8 49.3 + - - +
62A GLU* 3.2 20.6 + - - +
64A ALA* 1.3 77.1 - - + +
66A LEU* 1.3 66.4 + - + +
67A GLY 3.6 0.3 + - - -
285A ARG* 3.9 6.5 - - - +
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Residues in contact with LEU 66 (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 MSE 3.3 17.2 - - - +
62A GLU* 2.9 49.4 + - + +
63A ALA 4.0 3.1 - - - +
64A ALA 3.2 0.4 - - - -
65A LYS* 1.3 81.9 - - + +
67A GLY* 1.3 63.7 + - - +
68A VAL* 4.1 8.3 - - + -
288A LEU* 4.0 12.6 - - + -
289A ARG* 4.0 18.6 - - + -
292A VAL* 4.0 30.3 - - + +
296A LYS* 5.1 6.5 + - - +
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Residues in contact with GLY 67 (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 MSE 3.6 20.4 - - - +
63A ALA 3.8 0.4 - - - -
64A ALA* 3.0 15.7 + - - -
65A LYS 3.3 1.0 + - - -
66A LEU* 1.3 78.2 - - - +
68A VAL* 1.3 58.9 + - - +
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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