Contacts of the helix formed by residues 133 - 147 (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 ASN 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A THR 4.6 4.8 - - - +
132A ILE* 1.3 77.7 - - - +
134A LYS* 1.3 71.1 + - - +
135A ASN* 3.6 8.5 - - - +
136A SER* 2.7 40.9 + - - +
137A GLU 4.0 0.3 + - - -
613G G 2.8 58.4 + - - +
614G T 3.4 10.0 + - - -
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Residues in contact with LYS 134 (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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133A ASN* 1.3 77.8 - - + +
135A ASN* 1.3 62.9 + - - +
136A SER 2.8 4.0 + - - -
137A GLU* 3.3 12.6 + - - +
138A LYS* 3.8 29.4 + - - +
612G T 4.3 20.8 - - - +
613G G 3.6 29.3 + - - +
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Residues in contact with ASN 135 (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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2A LEU* 5.2 9.2 - - + +
133A ASN* 3.2 6.0 + - - +
134A LYS* 1.3 74.3 - - - +
136A SER* 1.3 54.9 + - - +
138A LYS* 3.0 33.9 + - + +
139A ARG* 2.6 48.4 + - + +
613G G 3.4 25.9 - - - +
614G T 3.5 21.6 + - - +
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Residues in contact with SER 136 (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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67A TRP* 3.9 10.5 - - - -
104A TYR* 4.3 3.1 + - - -
108A PHE* 3.4 21.8 - - - -
132A ILE* 3.1 24.2 - - - +
133A ASN* 2.7 51.4 + - - +
135A ASN* 1.3 70.8 - - - +
137A GLU* 1.3 56.5 + - - -
139A ARG* 3.4 7.0 - - - +
140A PHE* 2.8 25.8 + - - +
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Residues in contact with GLU 137 (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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67A TRP* 2.8 58.5 + - + +
133A ASN 4.0 0.2 + - - -
134A LYS 3.3 7.2 + - - +
136A SER* 1.3 76.6 - - - +
138A LYS* 1.3 57.9 + - + +
140A PHE* 3.7 5.6 - - - -
141A ASN* 2.6 58.5 + - - +
66E SER* 4.1 8.1 + - - -
68E ASP* 4.7 4.7 - - - +
69E ASP* 5.2 2.1 - - - +
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Residues in contact with LYS 138 (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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2A LEU* 3.8 16.6 - - + -
134A LYS* 3.8 26.1 + - - +
135A ASN* 3.0 33.1 + - - +
137A GLU* 1.3 73.5 - - + +
139A ARG* 1.3 69.7 + - - +
141A ASN* 3.7 6.3 - - - +
142A HIS* 2.9 27.4 + - - +
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Residues in contact with ARG 139 (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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2A LEU* 3.7 18.4 - - + +
3A GLY* 3.3 16.9 + - - +
4A ALA* 3.4 19.7 - - - +
5A ILE* 3.5 6.6 + - - +
6A ALA* 3.4 35.5 - - - +
7A TYR 4.8 0.2 - - - +
10A ASN* 5.8 1.4 - - - +
12A GLN* 3.1 30.3 + - - +
104A TYR* 5.3 0.4 - - - +
108A PHE* 6.1 3.6 - - + -
135A ASN* 2.6 37.8 + - + +
136A SER* 3.4 7.2 - - - +
138A LYS* 1.3 77.9 - - - +
140A PHE* 1.4 65.1 + - - +
142A HIS* 3.3 3.2 + - - +
143A PHE* 3.1 20.1 + - - +
614G T 2.7 37.2 + - - -
615G G 3.4 19.4 + - - -
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Residues in contact with PHE 140 (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 5.0 0.4 - - - -
62A LEU* 4.1 9.2 - - + -
65A VAL* 3.8 23.3 - - + -
66A SER* 3.8 5.2 - - - -
67A TRP* 3.4 53.4 - + + -
70A VAL* 4.0 9.0 - - + -
104A TYR* 3.3 26.0 + + - +
136A SER 2.8 16.1 + - - +
137A GLU 3.1 7.4 + - - +
139A ARG* 1.4 77.6 - - - +
141A ASN* 1.3 80.9 + - - +
143A PHE* 3.2 17.9 + + - +
144A LYS* 3.3 43.4 + - + +
68E ASP* 4.3 5.6 - - - -
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Residues in contact with ASN 141 (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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137A GLU* 2.6 43.7 + - - +
138A LYS* 3.7 6.5 - - - +
140A PHE* 1.3 79.6 - - - +
142A HIS* 1.3 68.6 + - - +
144A LYS* 2.7 20.7 + - - +
145A GLN* 3.0 26.1 + - - +
66E SER* 3.4 23.4 - - - -
68E ASP* 3.2 25.3 + - - -
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Residues in contact with HIS 142 (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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1A MET 4.1 15.7 - - - -
2A LEU* 3.5 32.2 + - + +
3A GLY 5.7 0.2 - - - +
40A LEU* 3.7 18.2 + - + +
41A ASN* 3.0 33.9 + - - -
138A LYS 2.9 18.8 + - - +
139A ARG 3.6 3.6 - - - +
141A ASN* 1.3 76.3 - - - +
143A PHE* 1.3 64.7 + - - +
145A GLN* 3.5 11.9 + - - -
146A ASN* 3.3 32.8 + - - +
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Residues in contact with PHE 143 (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* 3.7 24.0 - - + -
36A LEU* 3.6 21.5 - - + -
40A LEU* 3.4 21.7 - - + +
59A TYR* 3.8 24.5 - + + -
62A LEU* 3.6 32.1 - - + -
63A ILE* 4.1 8.7 - - + -
139A ARG 3.1 11.1 + - - +
140A PHE* 3.3 13.5 - + + +
141A ASN 2.8 4.0 + - - -
142A HIS* 1.3 73.9 - - - +
144A LYS* 1.3 65.8 + - + +
146A ASN 3.0 4.2 + - - -
147A CYS* 2.8 62.0 + - + +
152A PHE* 3.9 11.0 - + - -
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Residues in contact with LYS 144 (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 4.1 3.6 - - - +
63A ILE* 2.9 31.9 + - - +
64A ASN* 4.2 3.8 + - - +
65A VAL 3.1 17.6 + - - +
66A SER* 5.2 1.3 - - - +
140A PHE* 3.5 43.1 - - + +
141A ASN* 2.7 14.7 + - - +
143A PHE* 1.3 87.7 - - + +
145A GLN* 1.3 60.8 + - + +
146A ASN 3.3 0.4 + - - -
147A CYS* 4.0 16.3 + - - -
148A ASP* 4.7 1.2 - - - +
67E TRP* 6.2 0.2 - - - -
68E ASP* 5.6 2.7 - - - +
137E GLU* 3.9 32.7 + - - +
141E ASN* 3.6 13.7 + - - +
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Residues in contact with GLN 145 (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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141A ASN* 3.0 25.7 + - - +
142A HIS* 4.1 8.7 + - - +
143A PHE 3.2 0.2 + - - -
144A LYS* 1.3 79.9 - - + +
146A ASN* 1.3 71.2 + - - +
148A ASP* 3.8 3.6 - - - +
65E VAL 4.1 2.0 + - - -
66E SER* 3.8 22.2 - - - +
67E TRP* 4.3 2.1 - - + +
140E PHE* 3.7 11.8 - - + -
141E ASN* 3.4 23.9 - - - +
144E LYS* 3.4 39.6 + - + +
145E GLN* 2.9 24.4 + - - +
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Residues in contact with ASN 146 (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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40A LEU* 3.2 30.5 + - + +
41A ASN* 4.7 4.0 + - - -
142A HIS* 3.3 27.9 + - - +
143A PHE 3.0 2.4 + - - +
145A GLN* 1.3 95.9 - - - +
147A CYS* 1.3 56.8 + - - +
148A ASP 3.0 8.7 + - - -
149A LYS* 2.9 56.2 + - - +
150A ILE* 4.1 1.4 - - - +
144E LYS* 5.8 0.9 - - - +
145E GLN* 3.8 16.7 + - - +
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Residues in contact with CYS 147 (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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40A LEU* 4.1 0.8 - - - +
63A ILE* 4.3 25.9 - - + +
143A PHE* 2.8 56.9 + - + +
144A LYS* 4.0 20.0 - - - -
146A ASN* 1.3 70.3 - - - +
148A ASP* 1.3 62.0 + - - +
149A LYS 3.0 2.0 - - - -
150A ILE* 3.1 39.6 + - + +
152A PHE* 4.6 7.5 - - + -
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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