Contacts of the helix formed by residues 150 - 162 (chain A) in PDB entry 1F3Y
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ARG* 5.1 10.6 - - - +
41A GLN* 3.1 29.4 - - + +
44A GLN* 3.8 23.3 + - - +
146A THR* 4.0 0.9 - - - +
147A VAL* 2.7 29.5 + - + +
148A GLU 2.7 4.6 + - - -
149A PHE* 1.3 86.6 - - - +
151A LYS* 1.3 58.9 + - - +
152A PRO* 3.5 2.2 - - - -
153A VAL* 3.8 9.0 - - + -
154A TYR* 2.8 73.4 + - + +
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Residues in contact with LYS 151 (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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143A ILE* 3.0 40.0 - - + +
146A THR* 3.8 10.3 - - + +
147A VAL 2.9 9.8 + - - +
148A GLU* 3.7 30.7 - - - +
150A LYS* 1.3 78.4 - - - +
152A PRO* 1.3 71.7 - - + +
155A LYS* 2.7 40.4 + - + +
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Residues in contact with PRO 152 (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 GLY 4.1 15.3 - - - +
2A PRO* 5.9 0.9 - - + -
3A LEU* 4.2 9.2 - - + +
82A TYR* 3.7 26.7 - - + +
148A GLU 2.9 24.7 - - - +
150A LYS 3.7 0.4 - - - -
151A LYS* 1.3 92.7 - - + +
153A VAL* 1.3 64.2 + - + +
155A LYS* 3.5 9.1 - - + +
156A GLU* 3.1 24.3 + - - +
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Residues in contact with VAL 153 (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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3A LEU* 4.0 12.3 - - + -
80A LEU* 3.6 29.1 - - + +
82A TYR* 3.1 43.1 - - + -
105A GLN* 5.5 8.1 - - - +
107A TRP* 3.7 17.5 - - + +
149A PHE 3.7 9.6 - - - +
150A LYS* 3.6 7.2 - - + +
151A LYS 3.2 0.4 - - - -
152A PRO* 1.3 75.2 - - - +
154A TYR* 1.3 71.1 + - + +
156A GLU* 3.3 5.9 + - - +
157A VAL* 3.0 24.1 + - - +
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Residues in contact with TYR 154 (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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41A GLN* 3.3 13.6 + - - +
42A MET* 3.6 40.9 + - + -
44A GLN* 4.4 3.7 - - - +
107A TRP* 3.1 33.4 - + - -
142A LEU* 3.7 20.4 - - + -
143A ILE* 3.0 19.7 - - + -
146A THR* 3.4 26.9 - - + -
150A LYS* 2.8 50.5 + - + +
153A VAL* 1.3 79.3 - - + +
155A LYS* 1.3 53.1 + - - +
157A VAL* 2.9 10.7 + - - +
158A LEU* 2.7 38.6 + - + +
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Residues in contact with LYS 155 (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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140A GLU* 3.3 33.2 + - - +
143A ILE* 3.1 44.3 - - + +
151A LYS* 2.7 21.1 + - + +
152A PRO* 3.5 12.1 - - + +
154A TYR* 1.3 72.4 - - - +
156A GLU* 1.3 57.1 + - - +
158A LEU* 3.1 14.3 + - - +
159A SER* 3.0 27.5 + - - -
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Residues in contact with GLU 156 (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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3A LEU* 5.0 7.1 - - + +
5A SER* 3.8 13.3 + - - -
76A VAL* 6.1 0.2 - - - -
78A TYR* 2.7 50.7 + - + +
80A LEU* 4.1 12.3 - - + -
152A PRO 3.1 17.1 + - - +
153A VAL* 3.6 6.1 - - - +
154A TYR 3.2 0.2 - - - -
155A LYS* 1.3 76.0 - - - +
157A VAL* 1.3 59.7 + - - +
159A SER* 2.4 23.6 + - - +
160A VAL* 3.1 16.5 - - - +
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Residues in contact with VAL 157 (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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20A CYS* 4.8 0.7 - - - -
42A MET* 4.2 12.1 - - + -
76A VAL* 4.0 8.7 - - + -
80A LEU* 4.0 7.0 - - + -
107A TRP* 3.4 43.1 - - + -
153A VAL 3.0 16.1 + - - +
154A TYR* 2.9 16.3 + - - +
156A GLU* 1.3 78.0 - - - +
158A LEU* 1.3 55.1 + - + +
160A VAL* 3.3 5.0 + - - +
161A PHE* 3.0 67.8 + - + -
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Residues in contact with LEU 158 (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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20A CYS* 4.7 13.2 - - - -
28A ILE* 4.5 10.1 - - + -
42A MET* 5.7 1.1 - - + -
139A PRO* 3.2 54.7 - - + +
140A GLU* 3.8 2.7 - - + +
142A LEU* 5.7 2.9 - - + -
143A ILE* 3.3 20.4 - - + -
154A TYR* 2.7 21.1 + - + +
155A LYS* 3.5 16.6 - - - +
157A VAL* 1.3 72.6 - - + +
159A SER* 1.3 54.6 + - - +
161A PHE* 2.6 10.3 + - + +
162A ALA* 2.6 35.2 + - - -
165A LEU* 4.0 12.4 - - + +
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Residues in contact with SER 159 (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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78A TYR* 4.5 1.6 + - - -
155A LYS 3.0 9.9 + - - -
156A GLU* 2.4 36.4 + - - +
158A LEU* 1.3 73.6 - - - +
160A VAL* 1.3 63.2 + - - +
162A ALA* 3.2 22.1 + - - +
163A PRO* 3.7 2.8 - - - +
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Residues in contact with VAL 160 (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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75A GLU 3.8 7.4 - - - +
76A VAL* 3.8 21.8 - - + -
77A PRO* 3.2 38.1 - - + -
78A TYR* 3.8 16.4 - - + +
156A GLU 3.1 16.8 - - - +
157A VAL 3.3 7.8 + - - +
158A LEU 3.0 0.2 - - - -
159A SER* 1.3 77.4 + - - +
161A PHE* 1.3 63.7 - - + +
162A ALA 3.1 0.2 - - - -
163A PRO* 3.1 23.4 - - - +
164A HIS* 3.9 6.1 - - + +
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Residues in contact with PHE 161 (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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20A CYS* 3.3 26.0 - - + -
74A ALA* 4.0 6.1 - - + -
75A GLU 3.9 24.7 - - - -
76A VAL* 4.0 8.7 - - + -
108A PHE* 3.3 9.0 - - - -
109A LEU* 3.2 60.6 - - + -
157A VAL* 3.0 41.1 + - + +
158A LEU* 2.6 15.3 + - + +
160A VAL* 1.3 76.2 - - + +
162A ALA* 1.3 50.2 + - - -
163A PRO* 3.4 0.9 - - - -
164A HIS* 2.9 8.7 + - - -
165A LEU* 2.6 47.5 + - + +
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Residues in contact with ALA 162 (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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158A LEU 2.6 12.0 + - - +
159A SER* 3.2 20.2 - - - +
161A PHE* 1.3 72.7 - - - +
163A PRO* 1.3 64.2 - - + +
164A HIS 2.9 5.7 + - - -
165A LEU* 2.9 26.5 + - - +
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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