Contacts of the helix formed by residues 135 - 152 (chain A) in PDB entry 2F4W
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A THR* 1.3 77.0 - - - +
136A ASP* 1.3 61.2 + - - +
137A PHE* 3.3 35.8 - - - -
138A THR* 2.6 45.1 + - - +
139A LYS* 3.0 13.0 + - - +
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Residues in contact with ASP 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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55A PRO* 3.8 22.1 - - + +
125A LYS* 6.0 1.6 - - - +
134A THR 4.9 1.0 - - - +
135A SER* 1.3 75.3 - - - +
137A PHE* 1.3 66.6 + - + +
139A LYS* 3.7 16.1 - - - +
140A ARG* 2.9 54.8 + - - +
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Residues in contact with PHE 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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135A SER* 3.3 31.6 - - - -
136A ASP* 1.3 82.2 - - + +
138A THR* 1.3 61.1 + - - +
140A ARG* 3.8 14.3 - - + +
141A GLN* 3.1 24.6 + - - +
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Residues in contact with THR 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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134A THR* 3.3 20.0 - - - +
135A SER* 2.6 49.6 + - - +
137A PHE* 1.3 76.4 - - - +
139A LYS* 1.3 55.2 + - - +
141A GLN* 2.8 10.8 + - - +
142A LEU* 2.7 52.7 + - + +
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Residues in contact with LYS 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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55A PRO* 3.8 24.4 - - + +
56A TYR* 3.2 37.2 + - + +
61A TYR* 4.3 3.3 + - - -
84A ASN 3.9 16.3 - - - +
85A GLY* 3.7 13.0 + - - +
86A ARG* 4.2 9.9 - - - +
132A ILE 5.2 1.6 + - - -
134A THR* 3.4 37.3 + - - +
135A SER 3.0 10.4 + - - +
136A ASP* 3.7 17.3 - - - +
138A THR* 1.3 77.2 - - - +
140A ARG* 1.3 56.1 + - - +
142A LEU* 3.4 5.7 + - - +
143A ALA* 2.9 28.8 + - - +
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Residues in contact with ARG 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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54A THR 4.7 4.9 + - - -
55A PRO* 3.6 34.3 - - + +
57A GLU 6.1 0.7 - - - +
136A ASP* 2.9 56.5 + - - +
137A PHE* 3.9 13.7 - - + +
138A THR 3.2 0.2 - - - -
139A LYS* 1.3 76.0 - - - +
141A GLN* 1.3 61.1 + - - +
143A ALA* 3.4 4.6 + - - +
144A VAL* 3.1 26.5 + - - +
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Residues in contact with GLN 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 PHE 3.1 14.6 + - - +
138A THR* 2.8 16.9 + - - +
140A ARG* 1.3 69.2 - - - +
142A LEU* 1.3 53.9 + - + +
144A VAL* 3.1 18.8 + - - +
145A GLN* 2.7 66.2 + - - +
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Residues in contact with LEU 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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61A TYR* 4.7 1.1 - - - +
83A PRO* 3.8 32.0 - - + +
84A ASN* 3.5 9.6 - - - +
85A GLY* 3.3 35.9 - - - +
134A THR* 5.9 0.7 - - + -
138A THR* 2.7 35.4 + - - +
139A LYS 3.6 4.0 - - - +
141A GLN* 1.3 74.8 - - + +
143A ALA* 1.3 52.2 + - - +
145A GLN* 3.5 21.9 - - + +
146A SER* 2.7 35.3 + - - -
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Residues in contact with ALA 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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55A PRO 4.2 5.6 - - - +
56A TYR 4.0 1.8 - - - +
57A GLU 3.9 12.1 - - - +
58A GLY 3.8 7.2 - - - +
59A GLY* 3.7 21.5 - - - +
61A TYR* 3.3 23.5 + - - +
139A LYS 2.9 11.6 + - - +
140A ARG* 3.5 10.1 - - - +
141A GLN 3.2 0.2 - - - -
142A LEU* 1.3 71.0 - - - +
144A VAL* 1.3 66.2 + - + +
146A SER* 2.8 21.7 + - - -
147A LEU* 3.8 2.9 - - - +
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Residues in contact with VAL 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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140A ARG 3.1 16.9 + - - +
141A GLN* 3.1 20.7 + - - +
143A ALA* 1.3 79.7 - - + +
145A GLN* 1.3 63.0 + - + +
146A SER 3.2 0.9 + - - -
147A LEU* 3.5 21.3 + - + +
148A ALA* 4.5 1.4 + - - +
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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 GLN* 2.7 52.0 + - - +
142A LEU* 3.1 26.6 + - + +
144A VAL* 1.3 74.6 - - + +
146A SER* 1.3 63.0 + - - +
147A LEU 3.2 0.6 + - - -
148A ALA* 3.4 6.7 + - - +
149A PHE* 3.1 23.7 + - + +
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Residues in contact with SER 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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59A GLY* 3.6 1.2 - - - -
60A TYR 3.0 38.7 + - - -
61A TYR* 4.5 3.8 - - - -
82A THR* 3.6 15.3 - - - -
83A PRO 5.4 0.2 - - - -
142A LEU 2.7 18.5 + - - -
143A ALA* 2.8 20.6 + - - -
145A GLN* 1.3 73.7 - - - +
147A LEU* 1.3 65.6 + - - +
149A PHE* 4.1 7.2 - - - -
150A ASN* 2.9 30.3 + - - -
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Residues in contact with LEU 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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58A GLY 3.5 25.4 - - - +
60A TYR* 3.7 22.0 - - + -
143A ALA 3.8 4.9 - - - +
144A VAL* 3.5 13.4 + - + +
145A GLN 3.2 1.0 - - - -
146A SER* 1.3 90.8 + - - +
148A ALA* 1.3 60.3 + - - +
150A ASN* 4.1 1.4 - - - +
151A LEU* 3.0 32.6 + - + +
167A ILE* 3.7 35.2 - - + +
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Residues in contact with ALA 148 (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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144A VAL 4.5 1.3 + - - +
145A GLN* 3.4 7.8 + - - +
147A LEU* 1.3 76.4 - - - +
149A PHE* 1.3 66.0 + - - +
151A LEU* 3.4 9.6 + - - +
152A LYS* 3.2 41.6 + - - +
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Residues in contact with PHE 149 (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 HIS* 5.9 0.2 - - - -
81A ILE* 4.0 26.2 - - + -
82A THR* 4.0 7.0 - - + -
83A PRO* 3.7 38.8 - - + -
145A GLN* 3.1 18.4 + - + +
146A SER* 3.7 7.6 - - - +
148A ALA* 1.3 79.1 - - - +
150A ASN* 1.3 75.7 + - - +
152A LYS* 3.5 15.9 + - - +
153A ASP* 3.7 17.0 + - + +
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Residues in contact with ASN 150 (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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60A TYR* 2.6 43.6 + - - +
62A HIS* 3.8 8.0 + - - +
82A THR* 2.9 20.7 + - - -
146A SER* 2.9 23.6 + - - +
147A LEU 4.1 2.7 - - - +
149A PHE* 1.3 82.5 - - - +
151A LEU* 1.3 63.4 + - - +
153A ASP* 3.1 22.7 + - - +
156A PHE* 3.4 43.5 - - + -
157A CYS* 3.9 0.2 - - - -
167A ILE* 4.6 2.0 - - + +
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Residues in contact with LEU 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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147A LEU* 3.0 24.1 + - + +
148A ALA* 3.9 7.6 - - - +
149A PHE 3.4 0.2 - - - -
150A ASN* 1.3 78.5 - - - +
152A LYS* 1.3 57.2 + - + +
153A ASP 3.2 0.2 - - - -
156A PHE* 4.8 0.4 - - + -
157A CYS* 3.3 19.7 - - - -
164A VAL* 3.9 37.2 - - + +
167A ILE* 3.5 30.5 - - + -
168A LYS* 4.4 24.2 - - + +
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Residues in contact with LYS 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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148A ALA* 3.2 31.0 + - - +
149A PHE* 3.9 9.0 - - - +
150A ASN 3.3 0.2 - - - -
151A LEU* 1.3 76.5 - - + +
153A ASP* 1.3 56.9 + - - +
154A LYS* 3.3 17.4 + - - +
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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