Contacts of the helix formed by residues 44 - 56 (chain H) in PDB entry 1IB1
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 ASP 44 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212D LYS 5.6 0.2 - - - -
213D ASP 5.7 0.2 - - - +
215D THR* 3.3 26.6 + - - +
216D LEU* 4.4 1.8 + - - -
39H CYS 5.0 0.2 - - - +
40H LEU* 3.9 11.6 - - + -
41H THR* 2.8 43.5 + - - +
43H GLU* 1.3 76.5 - - - +
45H ALA* 1.3 62.8 + - - +
46H ALA 3.4 1.1 - - - -
47H GLY* 3.3 5.0 + - - -
48H VAL* 3.0 24.1 + - + +
74H LEU* 4.5 0.7 - - + -
85H PHE* 3.9 27.8 - - - -
90H LEU* 4.1 16.4 - - + +
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H THR 3.9 0.8 + - - -
42H PRO 3.2 10.6 + - - +
43H GLU 3.1 2.0 - - - -
44H ASP* 1.3 75.5 - - - +
46H ALA* 1.3 66.9 + - - +
48H VAL* 3.1 4.0 + - - +
49H PHE* 3.1 23.4 + - - +
67H LEU* 3.9 5.5 - - + +
70H VAL* 3.9 25.2 - - + +
71H GLN* 3.2 40.2 - - + +
74H LEU* 4.3 2.9 - - + +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LYS* 4.0 21.8 - - + +
43H GLU 4.2 7.8 + - - +
44H ASP 3.4 0.6 - - - -
45H ALA* 1.3 77.8 - - - +
47H GLY* 1.3 57.1 + - - +
49H PHE* 3.5 2.6 + - - +
50H GLU* 2.9 35.2 + - + +
67H LEU* 3.5 18.7 - - + +
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Residues in contact with GLY 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D TYR 5.3 0.2 - - - -
212D LYS* 3.4 27.9 + - - -
213D ASP* 4.8 8.0 - - - +
43H GLU 5.2 0.4 + - - -
44H ASP 3.3 7.6 + - - -
45H ALA 3.2 0.6 - - - -
46H ALA* 1.3 76.4 - - - +
48H VAL* 1.3 66.9 + - - +
50H GLU* 3.6 7.4 + - - +
51H ILE* 3.2 27.5 + - - +
90H LEU* 4.9 7.6 - - - -
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H LEU* 4.2 23.3 - - + -
44H ASP 3.0 20.9 - - - +
45H ALA* 3.1 8.0 + - - +
47H GLY* 1.3 75.8 - - - +
49H PHE* 1.3 58.0 + - - +
51H ILE* 2.9 22.6 + - - +
52H GLU* 2.9 25.4 + - - +
70H VAL* 3.9 19.1 - - + -
74H LEU* 4.9 1.1 - - + -
90H LEU* 4.3 7.9 - - + -
93H PHE* 3.6 42.1 - - + -
95H ILE* 4.3 5.4 - - + -
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Residues in contact with PHE 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H ALA 3.1 10.7 + - - +
46H ALA 3.8 3.4 - - - +
48H VAL* 1.3 80.6 - - - +
50H GLU* 1.3 69.1 + - - +
52H GLU* 3.1 12.4 + - + +
53H ARG* 2.9 49.0 + - + +
57H ILE* 3.7 31.4 - - + -
63H CYS* 4.0 10.8 - - - -
65H LEU 4.0 10.1 - - - -
66H ASN* 4.2 9.6 - - + -
67H LEU* 3.8 39.5 - - + +
70H VAL* 5.1 1.1 - - + +
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLU* 3.9 10.0 - - - +
211D TYR 5.1 2.2 - - - +
212D LYS* 3.5 42.0 + - + -
213D ASP* 6.1 0.9 - - - +
46H ALA* 2.9 20.4 + - + +
47H GLY* 3.8 8.3 - - - +
48H VAL 3.1 0.2 - - - -
49H PHE* 1.3 85.6 - - - +
51H ILE* 1.3 62.0 + - + +
53H ARG* 3.4 44.9 + - - +
54H GLU* 3.7 6.6 + - - +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ASP* 4.9 3.4 - - - +
47H GLY 3.2 16.8 - - - +
48H VAL* 2.9 7.1 + - - +
50H GLU* 1.3 77.2 - - + +
52H GLU* 1.3 59.4 + - - +
54H GLU* 3.2 9.6 + - + +
55H ALA* 2.9 30.5 + - + +
90H LEU* 4.2 22.2 - - + +
91H VAL 4.2 18.6 - - - +
92H ALA* 4.6 0.4 - - - +
93H PHE* 4.1 26.2 - - + -
125H ALA* 4.4 6.1 - - + -
126H VAL 4.1 9.4 - - - +
127H HIS* 3.9 36.8 - - + +
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Residues in contact with GLU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H VAL* 2.9 23.7 + - - +
49H PHE* 3.1 17.2 + - + +
51H ILE* 1.3 75.5 - - - +
53H ARG* 1.3 61.1 + - - +
56H PHE* 2.9 39.6 + - + +
57H ILE* 3.1 11.2 + - - +
63H CYS* 3.9 6.5 - - + +
64H PRO* 3.3 18.9 - - - +
65H LEU* 2.6 44.8 + - - +
70H VAL* 3.4 18.5 - - - +
93H PHE* 3.8 20.0 - - + -
123H ALA* 4.5 1.9 - - - +
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Residues in contact with ARG 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLU* 3.1 38.8 + - - +
49H PHE* 2.9 41.2 + - + +
50H GLU* 3.4 39.4 + - - +
52H GLU* 1.3 77.0 - - - +
54H GLU* 1.3 57.1 + - - +
57H ILE* 3.5 15.8 - - + +
58H SER* 3.1 27.0 + - - -
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H GLU 3.7 6.4 + - - +
51H ILE* 3.2 11.1 + - + +
52H GLU 3.2 0.2 - - - -
53H ARG* 1.3 79.3 - - - +
55H ALA* 1.3 66.3 + - - +
56H PHE 3.3 0.7 + - - -
58H SER* 2.6 32.2 + - - +
59H VAL* 4.6 1.6 - - - +
128H ARG* 3.4 34.3 + - + +
131H ARG* 2.8 39.2 + - - -
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Residues in contact with ALA 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H ILE* 2.9 19.7 + - + +
54H GLU* 1.3 76.4 - - - +
56H PHE* 1.3 72.1 + - + +
59H VAL* 4.0 12.6 - - - +
125H ALA* 4.2 10.5 - - + -
131H ARG* 3.3 28.3 - - - +
403H COT 3.7 27.6 - - + +
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Residues in contact with PHE 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H GLU* 2.9 34.2 + - + +
55H ALA* 1.3 80.9 - - + +
57H ILE* 1.3 69.0 + - - +
58H SER 2.8 4.2 + - - -
59H VAL* 2.8 16.2 + - - +
60H SER* 3.3 12.6 + - - -
62H ASN 3.2 15.9 - - - +
63H CYS* 3.6 6.1 - - + -
64H PRO* 3.4 34.3 - - + -
93H PHE* 4.7 2.9 - + - -
123H ALA* 4.8 0.7 - - + -
124H LEU 3.8 21.8 - - - -
125H ALA* 3.9 20.0 - - + -
403H COT 3.3 63.0 - + + -
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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