Contacts of the helix formed by residues 55 - 70 (chain A) in PDB entry 1IAP
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 ARG 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.8 27.8 - - + +
51A GLN 3.3 22.7 + - - +
52A VAL* 3.0 7.3 + - - +
53A LYS 3.5 0.2 - - - -
54A ARG* 1.3 113.4 + - - +
56A PRO* 1.3 59.0 - - - +
57A ALA 3.4 1.8 - - - -
58A HIS* 3.3 18.7 + - + -
59A LEU* 2.8 36.4 + - - +
183A ARG* 3.5 27.3 - - - +
186A TYR* 5.0 1.3 - - - -
187A GLU* 4.3 16.4 + - - +
190A GLU* 2.8 42.4 + - - +
229A LEU* 4.9 0.4 - - - -
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Residues in contact with PRO 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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54A ARG 3.2 12.3 - - - +
55A ARG* 1.3 83.3 - - - +
57A ALA* 1.3 58.3 + - - +
60A MET* 3.0 33.4 + - - +
190A GLU* 3.7 35.9 - - + +
191A ARG* 4.1 9.4 - - + +
194A ALA* 3.6 16.2 - - + -
226A MET* 3.7 6.2 - - + +
229A LEU* 4.0 24.0 - - + +
231A VAL* 3.7 17.5 - - + -
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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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55A ARG 3.4 0.4 - - - -
56A PRO* 1.3 77.7 - - - +
58A HIS* 1.3 68.9 + - + +
60A MET* 3.3 4.8 + - - +
61A ALA* 3.2 19.4 + - - +
172A LEU* 4.0 6.0 - - + +
175A LEU* 3.6 31.6 - - + -
190A GLU* 3.9 11.4 - - + +
193A VAL* 3.7 20.0 - - + -
194A ALA* 3.7 9.6 - - - +
197A LEU* 3.8 7.4 - - - +
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Residues in contact with HIS 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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45A GLN* 3.3 47.4 + - + +
46A PHE* 3.2 37.1 - + + -
52A VAL* 4.0 2.5 - - + -
55A ARG* 3.3 23.7 + - + +
57A ALA* 1.3 83.8 - - + +
59A LEU* 1.3 62.5 + - - +
61A ALA* 3.3 2.4 + - - +
62A LEU 3.1 17.2 + - - -
161A ARG* 5.1 4.5 - - - -
172A LEU* 3.7 33.5 - - + +
175A LEU* 4.1 16.1 - - + +
176A GLU* 6.1 2.2 - - + -
186A TYR* 4.3 6.9 + - - -
190A GLU* 4.4 7.9 - - - -
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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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52A VAL* 3.7 33.6 - - + +
53A LYS 4.1 9.2 - - - +
55A ARG 2.8 18.2 + - - +
56A PRO 3.8 4.3 - - - +
58A HIS* 1.3 78.3 - - - +
60A MET* 1.3 56.7 + - - +
62A LEU* 3.2 13.1 + - + +
63A LEU* 2.8 48.2 + - + +
75A LEU* 5.2 2.0 - - + -
79A LEU* 4.1 20.9 - - + -
225A TYR* 3.4 35.4 - - + -
226A MET* 3.7 13.0 - - + -
229A LEU* 4.2 2.5 - - + -
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Residues in contact with MET 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 PRO 3.0 21.7 + - - +
57A ALA 3.3 6.0 + - - +
59A LEU* 1.3 75.5 - - - +
61A ALA* 1.3 58.2 + - - +
63A LEU* 3.3 5.1 + - + +
64A GLN* 2.9 31.6 + - + +
168A TRP* 5.1 0.8 - - - -
194A ALA* 3.8 19.1 - - + +
197A LEU* 3.9 20.6 - - + +
198A LEU* 3.7 32.1 - - + +
201A LEU* 3.8 27.1 - - + -
222A ILE* 3.7 23.1 - - + -
226A MET* 3.7 23.1 - - + -
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Residues in contact with ALA 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 ALA 3.2 11.9 + - - +
58A HIS 3.6 8.5 - - - +
59A LEU 3.3 0.2 - - - -
60A MET* 1.3 76.2 - - - +
62A LEU* 1.3 63.4 + - - +
64A GLN 3.3 1.2 + - - -
65A HIS* 3.1 22.9 + - - +
157A PHE* 3.7 10.7 - - + -
167A PRO* 3.6 28.2 - - - +
168A TRP* 4.3 17.5 - - + -
172A LEU* 4.0 19.5 - - + -
197A LEU* 4.4 0.6 - - - +
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Residues in contact with LEU 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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46A PHE* 4.1 7.2 - - + -
52A VAL* 3.9 22.4 - - + -
58A HIS 3.1 12.4 + - - +
59A LEU* 3.4 12.8 - - + +
61A ALA* 1.3 77.0 - - - +
63A LEU* 1.3 56.6 + - - +
65A HIS* 3.2 3.8 + - - +
66A VAL* 2.9 45.2 + - + +
75A LEU* 4.0 24.2 - - + -
153A GLN* 4.6 4.3 - - + +
154A LEU* 3.6 31.6 - - + -
157A PHE* 3.7 36.9 - - + -
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Residues in contact with LEU 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* 2.8 46.6 + - + +
60A MET* 3.6 9.9 - - + +
62A LEU* 1.3 74.2 - - - +
64A GLN* 1.3 56.7 + - - +
66A VAL* 3.4 4.0 + - + +
67A ALA* 2.8 35.0 + - - +
72A PRO* 6.5 1.1 - - + -
75A LEU* 3.5 31.9 - - + -
76A LEU* 4.0 17.3 - - + -
79A LEU* 4.3 9.4 - - + -
201A LEU* 5.0 1.3 - - - -
222A ILE* 3.7 35.9 - - + -
225A TYR* 6.0 0.2 - - + -
226A MET* 4.2 12.8 - - + -
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Residues in contact with GLN 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 MET* 2.9 18.6 + - + +
61A ALA* 3.8 4.9 - - - +
63A LEU* 1.3 75.3 - - - +
65A HIS* 1.3 64.2 + - - +
67A ALA* 4.5 4.0 - - - -
68A LEU* 3.2 39.3 + - + +
167A PRO* 3.4 24.1 - - + +
168A TRP* 2.7 35.1 + - - +
197A LEU 4.9 1.8 + - - -
200A HIS* 4.5 12.3 + - - -
201A LEU* 4.5 32.8 - - + +
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Residues in contact with HIS 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 ALA 3.1 13.6 + - - +
62A LEU 3.3 7.9 - - - +
64A GLN* 1.3 75.3 - - - +
66A VAL* 1.3 63.2 + - + +
68A LEU* 3.1 4.4 + - - -
69A GLN* 2.9 51.0 + - + +
70A PHE* 4.0 12.7 - + - -
153A GLN 4.7 0.7 - - - -
156A ASP* 2.9 27.3 + - - -
157A PHE* 3.6 36.4 - + + -
160A LYS* 4.0 24.5 - - + -
165A MET 4.4 7.8 + - - -
166A THR* 4.2 8.6 - - + +
167A PRO* 4.3 12.4 - - + +
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Residues in contact with VAL 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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62A LEU* 2.9 32.0 + - + +
63A LEU* 3.9 4.3 - - + +
65A HIS* 1.3 80.7 - - + +
67A ALA* 1.3 59.1 + - - +
70A PHE* 2.8 45.0 + - + +
71A GLU 4.1 4.0 - - - +
72A PRO* 4.0 23.6 - - + -
75A LEU* 4.0 23.3 - - + -
153A GLN* 3.4 39.9 - - + +
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Residues in contact with ALA 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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63A LEU 2.8 23.6 + - - +
64A GLN* 4.0 6.3 - - - +
66A VAL* 1.3 73.2 - - - +
68A LEU* 1.3 64.7 + - + +
70A PHE 4.1 5.8 - - - +
72A PRO* 4.4 13.6 - - + +
201A LEU* 5.2 2.7 - - + -
208A ILE* 3.5 42.5 - - + +
214A LYS* 4.9 2.9 + - - -
218A VAL* 4.3 15.5 - - + -
222A ILE* 5.3 2.7 - - + -
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Residues in contact with LEU 68 (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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64A GLN* 3.2 35.2 + - + +
65A HIS* 3.1 3.8 + - - +
66A VAL 3.1 0.6 - - - -
67A ALA* 1.3 88.6 - - + +
69A GLN* 1.3 75.6 + - + +
70A PHE 5.0 0.2 - - - -
201A LEU* 4.9 4.5 - - + -
207A THR* 3.9 40.2 - - - +
208A ILE* 4.1 11.4 - - + -
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Residues in contact with GLN 69 (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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65A HIS* 2.9 38.6 + - + +
68A LEU* 1.3 103.5 + - + +
70A PHE* 1.3 85.5 + - + +
156A ASP* 5.2 0.4 - - - +
160A LYS* 4.3 14.1 + - - +
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Residues in contact with PHE 70 (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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65A HIS* 4.0 9.9 - + - -
66A VAL* 2.8 33.8 + - + +
67A ALA 4.1 5.9 - - - +
68A LEU 5.0 0.2 - - - -
69A GLN* 1.3 92.8 - - + +
71A GLU* 1.3 67.9 + - - +
72A PRO* 3.4 6.9 - - - +
152A ARG* 5.5 2.0 - - + -
153A GLN* 3.9 43.1 - - + +
156A ASP* 3.4 42.0 - - + -
160A LYS* 5.8 0.2 - - - -
214A LYS* 5.2 1.2 + - - -
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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
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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