Contacts of the helix formed by residues 49 - 67 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN* 3.6 10.3 - - - +
46B ASP* 3.5 28.3 + - - +
47B LEU 3.2 1.2 - - - -
48B SER* 1.3 78.0 - - - +
50B PRO* 1.3 71.2 - - + +
51B PHE* 4.4 2.5 - - + +
52B PHE* 3.0 38.5 + - + +
53B VAL* 3.1 13.3 + - - +
77B ASN* 5.7 0.8 + - - -
169B ASP* 3.0 32.9 + - - -
202B ASN 5.2 0.6 + - - -
203B SER* 3.7 18.5 + - - +
204B LYS* 4.4 5.3 - - - +
231B ASN* 4.7 2.1 + - - +
401B INS 2.6 26.6 + - - +
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Residues in contact with PRO 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER 3.6 7.6 - - - +
49B GLN* 1.3 85.2 - - + +
51B PHE* 1.3 62.8 + - - +
53B VAL* 3.4 10.2 + - + +
54B ALA* 3.2 22.9 + - - +
205B ARG* 5.1 3.8 - - - +
231B ASN* 6.2 0.4 - - - +
233B ASP* 3.4 42.0 - - + +
260B ILE* 5.1 15.0 - - + -
321B ARG* 5.0 1.4 + - - -
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLN* 3.2 2.1 + - + +
50B PRO* 1.3 80.5 - - - +
52B PHE* 1.3 81.4 + + + +
54B ALA* 3.4 5.7 + - - +
55B MSE 3.0 32.8 + - + +
125B ASP* 3.4 21.5 - - - -
258B ASP* 3.4 29.2 - - + +
260B ILE* 5.0 10.6 - - + +
278B GLN* 3.4 32.3 - - + -
280B PRO* 3.5 39.4 - - + +
321B ARG* 5.4 1.1 - - - +
401B INS 3.3 34.3 - - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.8 29.3 - + + -
45B ASN* 3.5 31.4 - - - -
46B ASP 4.1 12.6 - - - +
47B LEU* 3.7 8.4 - - + +
49B GLN* 3.0 39.4 + - + +
51B PHE* 1.3 99.4 - + - +
53B VAL* 1.3 59.5 + - - +
54B ALA 3.2 1.3 - - - -
55B MSE 3.6 13.0 - - - +
56B ARG* 2.8 30.8 + - - +
100B ALA* 4.5 6.1 - - + -
125B ASP* 3.4 35.7 - - + -
126B ARG* 4.0 8.1 - - - -
401B INS 4.2 3.1 - - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.2 35.4 - - + +
48B SER 4.7 2.0 - - - +
49B GLN 3.1 13.3 + - - +
50B PRO* 3.4 11.4 + - + +
52B PHE* 1.3 76.5 - - - +
54B ALA* 1.3 60.9 + - - +
56B ARG* 3.3 5.6 + - - +
57B ARG* 3.2 42.1 + - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PRO 3.2 8.1 + - - +
51B PHE 3.7 7.9 - - - +
53B VAL* 1.3 78.5 - - - +
55B MSE 1.3 65.0 + - - +
57B ARG* 3.1 38.4 + - - +
58B GLU* 3.3 17.2 + - - +
280B PRO* 6.4 1.8 - - + -
321B ARG* 3.4 35.4 - - - +
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Residues in contact with MSE 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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44B PHE* 4.0 12.6 - - + -
51B PHE* 3.0 31.2 + - + +
52B PHE* 3.2 27.8 + - - +
54B ALA* 1.3 74.7 - - - +
56B ARG* 1.3 59.3 + - - +
58B GLU* 3.1 11.2 + - - +
59B LEU* 2.9 24.3 + - - +
124B VAL* 4.5 10.1 - - + -
125B ASP* 4.4 6.1 - - + -
280B PRO* 3.6 44.1 - - + +
283B GLN* 4.2 17.7 - - + +
284B ILE* 3.6 32.3 - - + +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 4.1 17.9 - - + -
47B LEU* 3.6 32.6 - - + +
52B PHE 2.8 17.1 + - - +
53B VAL* 3.5 7.9 - - - +
54B ALA 3.2 0.2 - - - -
55B MSE 1.3 76.5 - - - +
57B ARG* 1.3 62.6 + - + +
59B LEU* 3.2 9.6 + - + +
60B GLU* 2.9 48.4 + - + +
72B VAL* 3.7 35.2 + - + +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.2 29.4 + - + +
54B ALA* 3.1 25.9 + - - +
56B ARG* 1.3 78.2 - - + +
58B GLU* 1.3 66.8 + - - +
60B GLU* 3.3 16.4 + - - +
61B ASP* 3.2 21.1 + - - +
321B ARG* 3.5 26.3 - - - +
324B GLU* 4.3 7.1 + - - -
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 3.6 14.3 - - - +
55B MSE 3.1 9.3 + - - +
57B ARG* 1.3 76.0 - - - +
59B LEU* 1.3 67.1 + - - +
61B ASP* 3.3 3.3 + - - +
62B GLU* 3.1 24.9 + - - +
281B GLY* 3.8 21.9 - - - +
284B ILE* 4.0 14.4 - - + -
285B ARG* 2.7 40.2 + - - +
321B ARG* 5.8 4.0 - - - +
324B GLU* 5.3 4.7 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 3.9 35.2 - - + -
44B PHE* 4.1 9.9 - - + -
55B MSE 2.9 12.9 + - - +
56B ARG* 3.3 11.4 - - + +
58B GLU* 1.3 78.3 - - - +
60B GLU* 1.3 58.5 + - + +
62B GLU* 3.4 3.7 + - - +
63B ALA* 2.8 28.6 + - - +
70B VAL* 4.2 12.1 - - + -
72B VAL* 3.8 28.7 - - + -
98B ILE* 5.2 0.2 - - + -
284B ILE* 3.7 29.7 - - + +
288B LEU* 4.0 24.5 - - + -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG* 2.9 50.4 + - + +
57B ARG* 3.7 17.2 - - - +
58B GLU 3.3 0.2 - - - -
59B LEU* 1.3 74.3 - - + +
61B ASP* 1.3 65.7 + - - +
63B ALA* 3.5 6.7 + - - +
64B ALA* 3.1 22.9 + - - +
70B VAL* 5.1 11.4 - - + -
72B VAL* 5.7 2.0 - - + +
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Residues in contact with ASP 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG 3.2 12.9 + - - +
58B GLU* 3.7 7.0 - - - +
59B LEU 3.3 0.2 - - - -
60B GLU* 1.3 76.3 - - - +
62B GLU* 1.3 61.6 + - - +
64B ALA* 3.2 8.4 + - - +
65B LYS* 2.8 48.4 + - - +
285B ARG* 2.7 34.8 + - - +
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Residues in contact with GLU 62 (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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58B GLU 3.1 13.8 + - - +
59B LEU* 3.9 3.8 - - - +
61B ASP* 1.3 80.0 + - - +
63B ALA* 1.3 61.8 + - - +
65B LYS* 3.2 15.1 + - - +
66B LEU* 2.9 54.1 + - + +
285B ARG* 2.8 47.8 + - + +
288B LEU* 3.9 9.9 - - + -
289B ARG* 2.8 45.6 + - - +
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Residues in contact with ALA 63 (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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59B LEU 2.8 18.1 + - - +
60B GLU* 3.8 5.2 - - - +
61B ASP 3.2 0.2 - - - -
62B GLU* 1.3 75.1 - - - +
64B ALA* 1.3 63.7 + - - +
66B LEU 3.3 0.7 + - - -
67B GLY* 3.1 3.8 + - - -
68B VAL* 3.0 46.2 + - + +
70B VAL* 3.7 32.5 - - + -
288B LEU* 3.6 10.0 - - + +
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Residues in contact with ALA 64 (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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60B GLU 3.1 13.7 + - - +
61B ASP* 3.5 9.6 - - - +
63B ALA* 1.3 76.5 - - - +
65B LYS* 1.3 62.6 + - + +
67B GLY* 3.1 14.7 + - - -
68B VAL 5.1 0.4 - - - -
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Residues in contact with LYS 65 (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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61B ASP* 2.8 50.8 + - - +
62B GLU* 3.2 21.4 + - - +
64B ALA* 1.3 77.3 - - + +
66B LEU* 1.3 66.4 + - + +
67B GLY 3.6 0.5 + - - -
285B ARG* 3.9 5.5 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B MSE 3.3 17.8 - - - +
62B GLU* 2.9 49.2 + - + +
63B ALA 4.1 2.9 - - - +
64B ALA 3.2 0.4 - - - -
65B LYS* 1.3 80.8 - - + +
67B GLY* 1.3 63.9 + - - +
68B VAL* 4.2 7.9 - - + -
288B LEU* 4.0 13.2 - - + -
289B ARG* 4.1 21.5 - - + -
292B VAL* 3.8 31.0 - - + +
296B LYS* 5.1 5.5 + - - +
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Residues in contact with GLY 67 (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 MSE 3.6 20.4 - - - +
63B ALA 3.7 0.4 - - - -
64B ALA* 3.1 15.8 + - - -
65B LYS 3.3 1.0 + - - -
66B LEU* 1.3 78.0 - - - +
68B VAL* 1.3 59.4 + - - +
69B LYS 4.3 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
------------------------------------------------------------
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