Contacts of the helix formed by residues 52 - 63 (chain B) in PDB entry 1YFJ
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 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B TYR* 3.9 12.9 + - - -
50B ASP* 3.0 15.0 + - - +
51B ILE* 1.3 74.8 - - - +
53B GLU* 1.3 66.3 - - - +
54B PRO* 3.3 7.1 - - + +
55B ILE* 3.0 33.8 + - + +
56B ILE* 3.2 11.4 + - - +
115B ILE 4.4 13.1 + - - +
117B ILE* 4.6 21.7 + - - +
180B ASP* 5.3 3.1 + - - +
181B TYR* 4.1 10.9 - - - +
183B LYS* 5.2 2.7 + - - -
184B PHE* 3.7 35.4 - - + -
402B SAH 3.2 22.1 + - - +
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Residues in contact with GLU 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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51B ILE 3.0 9.4 + - - +
52B GLN* 1.3 71.1 - - - +
54B PRO* 1.3 66.7 - - + +
56B ILE* 3.0 2.8 + - + -
57B GLU* 2.7 51.4 + - + +
154B SER* 3.7 29.1 + - - +
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Residues in contact with PRO 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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52B GLN* 3.3 9.2 - - + +
53B GLU* 1.3 93.4 - - + +
55B ILE* 1.3 55.8 + - - +
57B GLU* 3.3 8.8 + - + +
58B MET* 2.8 26.7 + - - +
94B TYR* 3.8 17.5 - - - +
100B PRO* 5.2 1.4 - - - +
103B LEU* 3.6 7.8 - - + +
117B ILE* 3.3 44.0 - - + -
121B GLY* 5.5 3.1 - - - +
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Residues in contact with ILE 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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5B ILE* 4.9 3.8 - - + -
7B TYR* 3.9 29.8 - - + +
34B GLY 4.4 5.2 - - - +
50B ASP* 5.6 3.6 - - + +
52B GLN* 3.0 32.0 + - + +
54B PRO* 1.3 75.5 - - - +
56B ILE* 1.3 68.2 + - + +
58B MET* 3.2 14.7 + - + +
59B TYR* 3.0 54.5 + - + +
103B LEU* 4.6 1.8 - - + -
115B ILE* 3.9 38.4 - - + +
117B ILE* 5.1 2.0 - - + -
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Residues in contact with ILE 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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33B CYS* 3.8 26.9 - - - -
48B ALA 4.3 0.9 - - - +
50B ASP* 3.7 20.2 - - + +
52B GLN 3.2 6.2 + - - +
53B GLU* 3.0 7.9 + - + +
55B ILE* 1.3 77.6 - - + +
57B GLU* 1.3 61.3 + - - +
59B TYR* 3.4 18.4 + - + +
60B LYS* 3.1 34.1 + - + +
152B PHE* 3.9 23.6 - - + -
153B SER* 3.4 37.0 - - - +
154B SER* 3.9 9.4 - - - +
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Residues in contact with GLU 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 GLU* 2.7 41.0 + - + +
54B PRO* 3.6 7.6 - - + +
56B ILE* 1.3 76.1 - - - +
58B MET* 1.3 67.6 + - - +
60B LYS* 3.4 30.8 + - - +
61B ARG* 3.0 23.6 + - - +
100B PRO* 3.6 18.2 - - + +
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Residues in contact with MET 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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5B ILE* 4.2 13.0 - - + -
54B PRO 2.8 14.3 + - - +
55B ILE* 3.3 21.3 - - + +
57B GLU* 1.3 78.6 - - - +
59B TYR* 1.3 86.3 + - + +
61B ARG* 3.2 4.3 + - - +
62B LEU* 2.9 32.8 + - + +
100B PRO* 3.6 27.1 - - - +
103B LEU* 3.9 16.2 - - + +
104B TYR* 3.5 49.4 - - + -
107B HIS* 5.5 0.7 - - - +
115B ILE* 4.5 11.7 - - + -
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Residues in contact with TYR 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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4B ALA* 3.8 18.8 - - + -
5B ILE* 3.6 12.6 - - + +
34B GLY 2.8 27.9 + - - -
35B GLY* 3.3 15.2 + - - -
36B LEU* 3.6 29.6 - - + -
55B ILE* 3.0 32.4 + - + +
56B ILE* 3.7 20.2 - - + +
57B GLU 3.2 0.4 - - - -
58B MET* 1.3 95.1 - - + +
60B LYS* 1.3 64.9 + - - +
62B LEU* 3.0 21.0 + - + +
63B ILE* 3.3 16.9 + - - +
143B PHE* 3.6 11.5 - + + -
152B PHE* 3.8 25.1 - + + -
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Residues in contact with LYS 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 ILE* 3.1 24.4 + - + +
57B GLU* 3.4 31.0 + - - +
59B TYR* 1.3 75.7 - - - +
61B ARG* 1.3 61.6 + - - +
63B ILE* 3.4 26.9 - - + +
64B ASN* 4.2 6.1 - - - +
152B PHE* 3.9 34.8 + - + +
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Residues in contact with ARG 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 GLU 3.0 17.3 + - - +
58B MET 3.5 4.9 - - - +
60B LYS* 1.3 74.7 - - - +
62B LEU* 1.3 67.0 + - + +
63B ILE 3.1 1.8 - - - -
64B ASN* 3.1 16.4 + - - +
65B VAL* 3.4 23.5 - - + +
99B ASP* 2.5 37.5 + - - -
100B PRO* 3.6 22.9 - - + +
101B LEU* 3.8 30.8 - - + +
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Residues in contact with LEU 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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4B ALA* 5.7 2.2 - - + -
58B MET* 2.9 28.3 + - + +
59B TYR* 3.0 15.4 + - + +
61B ARG* 1.3 78.9 - - + +
63B ILE* 1.3 63.9 + - - +
64B ASN 2.9 1.4 + - - -
65B VAL* 2.9 40.5 + - + +
101B LEU* 4.5 7.0 - - + -
104B TYR* 3.5 58.3 - - + +
140B PHE* 4.7 6.0 - - + -
143B PHE* 3.6 25.6 - - + -
144B LYS* 3.7 7.4 - - - +
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Residues in contact with ILE 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 TYR 3.3 7.4 + - - +
60B LYS* 3.4 23.8 - - + +
62B LEU* 1.3 76.7 - - - +
64B ASN* 1.3 76.5 + - - +
143B PHE* 3.9 10.7 - - + -
144B LYS* 3.0 21.5 + - - +
147B CYS* 4.3 23.6 - - + +
148B ASP* 5.4 5.2 - - - +
150B ILE 5.7 1.6 - - - +
152B PHE* 4.0 25.1 - - + -
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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