Contacts of the helix formed by residues 46 - 62 (chain B) in PDB entry 5I7L
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 GLY 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B THR* 1.3 87.0 + - - +
47B LEU* 1.3 61.7 + - - -
48B CYS 3.3 2.6 + - - -
49B GLY 3.8 1.3 + - - -
50B SER* 2.8 30.0 + - - -
252B PHE 6.1 0.4 - - - -
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Residues in contact with LEU 47 (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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46B GLY* 1.3 72.5 - - - -
48B CYS* 1.3 54.2 + - - +
50B SER* 3.6 4.1 - - - -
51B LEU* 2.6 39.9 + - - +
238B LEU* 3.8 20.2 - - + +
241B ASP* 3.6 37.2 - - + +
242B ILE* 4.0 9.2 - - + +
245B MET* 3.5 39.0 - - + -
252B PHE* 3.5 26.7 + - + +
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Residues in contact with CYS 48 (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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46B GLY 3.3 0.6 - - - -
47B LEU* 1.3 79.7 - - - +
49B GLY* 1.3 58.0 + - - +
51B LEU* 3.7 2.1 - - - +
52B THR* 2.9 35.4 + - - +
120B LEU* 3.9 16.3 - - - +
252B PHE* 3.3 22.0 + - - +
253B CYS* 2.0 53.2 - - - -
254B ILE 5.2 0.2 - - - -
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Residues in contact with GLY 49 (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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45B THR* 4.0 16.4 + - - +
46B GLY 3.8 3.2 + - - -
47B LEU 3.5 0.2 - - - -
48B CYS* 1.3 76.6 - - - +
50B SER* 1.3 64.2 + - - +
52B THR* 3.4 9.1 + - - -
53B ASN* 3.0 33.1 + - - -
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Residues in contact with SER 50 (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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45B THR* 3.3 18.9 + - - +
46B GLY 2.8 24.2 + - - -
47B LEU* 3.6 5.2 - - - -
49B GLY* 1.3 75.3 - - - +
51B LEU* 1.3 61.9 + - - +
53B ASN* 3.5 5.3 + - - +
54B ALA* 3.0 28.8 + - - +
238B LEU* 4.1 21.2 - - - +
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Residues in contact with LEU 51 (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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47B LEU 2.6 21.8 + - - +
48B CYS 3.7 3.6 - - - +
50B SER* 1.3 74.7 - - - +
52B THR* 1.3 57.2 + - - +
54B ALA* 3.1 3.6 + - - +
55B LEU* 2.8 45.4 + - + +
120B LEU* 3.6 26.0 - - + -
129B LEU* 3.7 22.2 - - + -
163B ILE* 4.8 5.4 - - + -
175B LEU* 4.7 3.4 - - + -
231B LEU* 5.1 1.1 - - + -
234B LEU* 3.5 35.7 - - + -
238B LEU* 4.4 4.9 - - + +
242B ILE* 3.8 25.6 - - + -
252B PHE* 5.3 1.3 - - + -
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Residues in contact with THR 52 (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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48B CYS* 2.9 23.5 + - - +
49B GLY* 3.4 11.8 + - - -
51B LEU* 1.3 75.7 - - - +
53B ASN* 1.3 62.1 + - - +
55B LEU* 4.4 6.7 - - - -
56B SER* 2.9 30.5 + - - -
118B LEU* 3.5 24.8 - - + +
119B GLY 4.8 0.2 - - - -
120B LEU* 3.5 43.3 - - + +
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Residues in contact with ASN 53 (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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43B SER 5.5 3.8 + - - -
45B THR* 5.2 5.5 - - - +
49B GLY* 3.0 24.2 + - - +
50B SER* 3.8 4.8 - - - +
52B THR* 1.3 81.7 + - - +
54B ALA* 1.3 56.4 + - - +
56B SER* 3.7 6.3 - - - -
57B ASN* 2.8 40.4 + - - +
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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
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50B SER 3.0 18.7 + - - +
51B LEU 3.5 4.7 - - - +
53B ASN* 1.3 75.2 - - - +
55B LEU* 1.3 66.6 + - - +
57B ASN* 3.2 8.8 + - - +
58B GLY* 2.9 22.2 + - - -
230B VAL* 4.1 4.7 - - - +
234B LEU* 3.8 21.8 - - + -
238B LEU* 4.4 11.9 - - + -
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Residues in contact with LEU 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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51B LEU* 2.8 38.7 + - + +
52B THR* 4.4 2.0 - - - -
54B ALA* 1.3 75.1 - - - +
56B SER* 1.3 65.4 + - - +
58B GLY* 3.8 0.3 - - - -
59B LEU* 3.1 32.2 + - + +
118B LEU* 3.6 15.9 - - + -
120B LEU* 4.3 8.7 - - + -
131B VAL* 3.8 29.8 - - + -
133B ILE* 6.5 0.2 - - + -
163B ILE* 4.3 9.4 - - + -
227B VAL* 5.3 7.2 - - + +
230B VAL* 4.0 19.0 - - + +
231B LEU* 3.6 31.0 - - + -
234B LEU* 4.9 2.0 - - + -
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Residues in contact with SER 56 (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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52B THR 2.9 18.8 + - - -
53B ASN* 3.8 7.6 - - - -
55B LEU* 1.3 77.6 - - - +
57B ASN* 1.3 62.6 + - - +
59B LEU* 3.9 1.3 - - - +
60B LEU* 3.3 31.9 + - - +
115B LEU* 3.8 17.7 - - - +
116B LEU 5.5 0.5 + - - -
118B LEU* 3.6 16.7 - - - +
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Residues in contact with ASN 57 (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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53B ASN* 2.8 31.5 + - - +
54B ALA* 3.2 6.6 + - - +
56B SER* 1.3 73.3 + - - +
58B GLY* 1.3 58.5 + - - +
60B LEU* 3.5 6.9 + - - +
61B SER* 2.9 36.4 + - - +
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Residues in contact with GLY 58 (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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54B ALA 2.9 15.9 + - - -
57B ASN* 1.3 73.5 - - - +
59B LEU* 1.3 54.9 + - - +
61B SER* 3.4 3.7 - - - -
62B GLY* 2.5 36.6 + - - -
230B VAL* 3.3 25.4 - - - +
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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
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55B LEU* 3.1 26.0 + - + +
56B SER 3.9 3.1 - - - +
58B GLY* 1.3 75.3 - - - +
60B LEU* 1.3 63.2 + - - +
62B GLY* 3.1 7.3 + - - -
63B GLY 3.3 0.2 + - - -
64B LEU* 3.0 40.4 + - + +
115B LEU* 4.2 16.6 - - + -
118B LEU* 4.8 6.1 - - + -
133B ILE* 3.8 38.4 - - + -
223B VAL* 5.3 0.7 - - + -
226B LEU* 3.8 23.3 - - + +
227B VAL* 3.8 26.0 - - + -
230B VAL* 3.5 11.8 - - + +
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Residues in contact with LEU 60 (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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56B SER* 3.3 23.2 + - - +
57B ASN* 4.0 6.5 - - - +
59B LEU* 1.3 78.9 - - - +
61B SER* 1.3 61.4 + - - +
63B GLY* 3.4 11.1 + - - -
64B LEU* 4.4 3.9 + - + +
65B LEU* 3.8 36.1 + - + +
115B LEU* 3.9 29.4 - - + +
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Residues in contact with SER 61 (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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57B ASN* 2.9 22.6 + - - +
58B GLY* 4.0 3.8 - - - -
60B LEU* 1.3 74.5 - - - +
62B GLY* 1.3 57.8 + - - +
63B GLY 3.1 8.7 + - - -
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Residues in contact with GLY 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 GLY 2.5 23.0 + - - -
59B LEU 3.1 2.6 + - - -
61B SER* 1.3 73.6 - - - +
63B GLY* 1.3 60.6 + - - +
64B LEU 3.4 3.1 - - - -
67B ILE* 4.6 4.0 - - - +
226B LEU* 3.6 26.7 - - - +
229B GLU* 5.0 6.7 - - - +
230B VAL* 5.6 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
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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