Contacts of the helix formed by residues 52 - 63 (chain A) in PDB entry 1YFL
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.8 12.9 + - - -
50A ASP* 3.2 5.5 + - - +
51A ILE* 1.3 72.5 - - + +
53A GLU* 1.3 67.0 + - - +
54A PRO* 3.1 8.9 - - + +
55A ILE* 3.0 36.7 + - + +
56A ILE* 3.0 15.0 + - - +
115A ILE 4.5 11.3 + - - +
117A ILE* 4.7 15.8 - - - +
180A ASP* 5.4 2.7 + - - +
181A TYR* 4.1 9.7 - - - +
183A LYS* 4.6 5.5 + - - -
184A PHE* 3.5 34.1 - - + -
300A SFG 3.1 26.1 + - - +
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Residues in contact with GLU 53 (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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51A ILE 3.0 10.4 + - - +
52A GLN* 1.3 70.9 - - - +
54A PRO* 1.3 72.1 - - + +
56A ILE* 3.5 1.1 - - - -
57A GLU* 2.6 48.9 + - + +
154A SER* 3.6 35.4 + - - +
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Residues in contact with PRO 54 (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 GLN* 3.2 9.9 - - + +
53A GLU* 1.3 95.0 - - + +
55A ILE* 1.3 59.1 + - + +
57A GLU* 3.7 6.3 - - + +
58A MET* 2.8 29.3 + - - +
94A TYR* 3.8 17.2 + - - +
98A ARG* 6.2 1.3 - - - +
100A PRO* 5.6 0.5 - - - +
103A LEU* 3.7 8.7 - - + +
117A ILE* 3.3 42.4 - - + -
121A GLY* 5.5 4.3 - - - +
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Residues in contact with ILE 55 (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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5A ILE* 4.3 7.6 - - + -
7A TYR* 3.9 22.9 - - + +
34A GLY* 4.6 5.8 - - - +
50A ASP* 5.8 2.9 - - - +
52A GLN* 3.0 40.2 + - + +
54A PRO* 1.3 79.0 - - + +
56A ILE* 1.3 63.0 + - + +
58A MET* 3.4 19.2 - - + +
59A TYR* 3.2 49.2 + - + +
103A LEU* 4.4 2.5 - - + -
115A ILE* 4.0 32.5 - - + +
117A ILE* 5.4 0.2 - - + -
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Residues in contact with ILE 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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33A CYS* 4.2 8.5 - - - -
34A GLY* 6.3 0.2 - - - -
48A ALA 4.6 0.2 - - - +
50A ASP* 3.7 40.4 - - + +
52A GLN 3.0 15.5 + - - +
53A GLU 3.7 5.4 - - - +
55A ILE* 1.3 78.3 - - + +
57A GLU* 1.3 64.8 + - - +
59A TYR* 3.2 26.7 + - + +
60A LYS* 3.1 31.9 + - + +
152A PHE* 4.0 25.8 - - + -
153A SER 3.8 12.1 - - - +
154A SER* 3.8 21.1 - - - +
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Residues in contact with GLU 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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53A GLU* 2.6 45.4 + - + +
54A PRO* 3.7 4.9 - - + +
56A ILE* 1.3 70.4 - - - +
58A MET* 1.3 60.9 + - - +
60A LYS* 3.0 44.8 + - - +
61A ARG* 2.8 31.5 + - - +
100A PRO* 3.9 19.1 - - + +
154A SER* 4.8 1.0 + - - -
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Residues in contact with MET 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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5A ILE* 3.9 31.0 - - + -
54A PRO 2.8 17.1 + - - +
55A ILE* 3.4 11.0 - - + +
57A GLU* 1.3 78.7 - - - +
59A TYR* 1.3 82.5 + - + +
61A ARG* 3.5 1.6 - - - +
62A LEU* 3.0 34.1 + - + +
100A PRO* 3.8 27.5 - - - +
103A LEU* 3.9 20.0 - - + +
104A TYR* 3.6 40.4 - - + -
107A HIS* 5.3 1.1 - - + -
115A ILE* 4.9 7.0 - - + -
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Residues in contact with TYR 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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4A ALA* 4.3 12.1 - - + -
5A ILE* 3.8 11.3 - - + +
33A CYS* 5.2 0.2 - - - -
34A GLY 2.4 34.1 + - - -
35A GLY 3.9 3.3 + - - -
36A LEU* 3.5 27.9 - - + +
55A ILE* 3.2 29.5 - - + +
56A ILE* 3.2 20.6 + - + +
57A GLU 3.0 0.2 - - - -
58A MET* 1.3 96.1 - - + +
60A LYS* 1.3 69.6 + - - +
61A ARG 2.9 2.2 + - - -
62A LEU* 3.2 15.4 + - + +
63A ILE* 3.2 15.2 + - - +
143A PHE* 3.8 14.0 - + + -
152A PHE* 3.6 38.4 - + + -
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Residues in contact with LYS 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 ILE* 3.2 22.9 - - + +
57A GLU* 3.0 44.6 + - - +
59A TYR* 1.3 78.8 - - - +
61A ARG* 1.3 67.3 + - - +
63A ILE* 3.4 24.8 - - - +
64A ASN* 4.0 4.3 - - - +
152A PHE* 4.4 28.2 + - + +
154A SER* 5.0 4.4 + - - -
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Residues in contact with ARG 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 GLU 2.8 17.0 + - - +
58A MET 3.5 5.6 - - - +
59A TYR 2.9 0.2 - - - -
60A LYS* 1.3 75.8 - - - +
62A LEU* 1.3 56.6 + - - +
63A ILE 2.4 18.9 + - - -
64A ASN* 2.9 19.1 + - - +
65A VAL* 4.0 19.7 + - + +
99A ASP* 2.5 32.7 + - - -
100A PRO* 3.5 21.6 - - + +
101A LEU* 3.1 35.7 - - + +
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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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4A ALA* 5.9 1.6 - - + -
5A ILE* 5.5 0.4 - - + -
58A MET* 3.0 32.2 + - + +
59A TYR* 3.6 14.8 - - + +
61A ARG* 1.3 75.9 - - + +
63A ILE* 1.3 63.0 + - - +
64A ASN 2.9 2.1 + - - -
65A VAL* 3.0 47.8 + - + +
101A LEU* 4.7 4.7 - - + -
104A TYR* 3.3 60.6 - - + -
140A PHE* 4.1 7.2 - - + -
143A PHE* 3.6 22.2 - - + -
144A LYS* 4.1 7.6 - - - +
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Residues in contact with ILE 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 TYR 3.2 9.8 + - - +
60A LYS* 3.4 26.2 - - - +
61A ARG 2.4 12.5 + - - -
62A LEU* 1.3 68.3 - - - +
64A ASN* 1.3 73.4 + - - +
143A PHE* 4.1 8.0 - - + -
144A LYS* 2.9 24.3 + - - +
147A CYS* 4.3 25.1 - - - +
150A ILE 6.2 0.2 - - - +
152A PHE* 4.8 13.0 - - + -
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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