Contacts of the helix formed by residues 139 - 155 (chain A) in PDB entry 3HF8
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASP* 1.3 81.4 + - + +
140A VAL* 1.3 68.0 + - + +
141A TYR 3.2 1.5 - - - +
142A ARG* 3.3 18.0 + - - +
143A LYS* 3.1 32.4 + - - +
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 3.1 9.1 + - - +
139A ASN* 1.3 76.6 - - + +
141A TYR* 1.3 62.7 + - - +
143A LYS* 3.5 8.1 + - - +
144A ARG* 3.1 24.8 + - + +
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Residues in contact with TYR 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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138A ASP* 3.0 35.0 + - - +
140A VAL* 1.3 78.8 - - - +
142A ARG* 1.3 60.7 + - + +
144A ARG* 3.4 9.5 + - + +
145A ARG* 2.9 75.2 + - + +
255A TYR* 4.6 0.9 - - - -
256A VAL 3.4 24.4 + - - -
257A ARG* 4.7 1.0 - - - -
258A HIS* 3.7 43.6 + + + +
267A GLU* 4.1 3.3 + - - -
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Residues in contact with ARG 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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138A ASP 4.4 19.0 + - - +
139A ASN* 3.3 18.9 + - - +
140A VAL 3.3 0.2 - - - -
141A TYR* 1.3 81.8 - - + +
143A LYS* 1.3 60.0 + - + +
145A ARG* 3.4 7.2 + - - +
146A LYS* 3.1 27.7 + - - +
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Residues in contact with LYS 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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139A ASN* 3.1 23.7 + - - +
140A VAL* 3.9 6.7 - - - +
141A TYR 3.4 0.2 - - - -
142A ARG* 1.3 75.2 - - + +
144A ARG* 1.3 58.7 + - - +
146A LYS* 3.4 9.3 + - - +
147A TYR* 3.0 25.3 + - - +
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Residues in contact with ARG 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 VAL* 3.1 20.0 + - + +
141A TYR* 3.7 12.3 - - + +
143A LYS* 1.3 75.2 - - - +
145A ARG* 1.3 63.9 + - + +
147A TYR* 3.3 30.9 - - - +
148A PHE* 3.2 43.1 + - + -
164A VAL* 3.8 10.1 - - - +
165A GLU 3.0 26.7 + - - -
166A PHE* 3.6 3.0 - - - +
167A THR* 3.8 17.0 - - + +
170A GLU* 2.8 42.9 + - - +
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Residues in contact with ARG 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 TYR* 2.9 67.2 + - + +
142A ARG* 3.8 7.4 - - - +
144A ARG* 1.3 76.5 - - + +
146A LYS* 1.3 58.9 + - - +
148A PHE* 3.4 5.5 + - - +
149A ALA* 2.9 29.3 + - - +
233A ALA 5.2 3.6 + - - -
234A GLY* 6.0 1.2 - - - -
255A TYR* 3.3 52.4 + - - -
267A GLU* 2.5 42.4 + - - -
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Residues in contact with LYS 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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142A ARG 3.1 17.5 + - - +
143A LYS* 3.5 10.1 - - - +
144A ARG 3.2 0.2 - - - -
145A ARG* 1.3 73.6 - - - +
147A TYR* 1.3 61.2 + - - +
149A ALA* 3.7 7.1 - - + +
150A ASP* 2.8 67.1 + - - +
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Residues in contact with TYR 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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143A LYS 3.0 13.2 + - - +
144A ARG* 3.3 41.7 - - - +
146A LYS* 1.3 77.2 - - - +
148A PHE* 1.3 72.0 + + - +
150A ASP* 3.8 6.3 - - - +
151A LEU* 3.2 57.5 + - + +
163A LYS 4.7 2.9 + - - -
164A VAL* 4.0 26.1 - - + +
165A GLU 5.0 1.6 + - - -
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Residues in contact with PHE 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 ARG* 3.2 49.8 + - + -
145A ARG* 3.8 5.8 - - - +
146A LYS 3.3 0.2 - - - -
147A TYR* 1.3 82.7 - + - +
149A ALA* 1.3 65.1 + - - +
151A LEU* 3.2 7.4 + - + +
152A ALA* 3.2 21.5 + - - +
164A VAL* 3.6 35.0 - - + -
166A PHE* 3.7 21.1 - + - -
170A GLU* 3.8 7.9 - - - -
232A VAL 5.6 0.2 - - - +
233A ALA* 5.6 0.7 - - - -
254A GLN* 3.4 41.9 - - + +
255A TYR* 3.5 37.5 - - + +
256A VAL 4.8 0.4 - - - -
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Residues in contact with ALA 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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145A ARG 2.9 19.1 + - - +
146A LYS* 3.7 10.1 - - + +
147A TYR 3.4 0.2 - - - -
148A PHE* 1.3 75.6 - - - +
150A ASP* 1.3 60.7 + - - +
152A ALA* 3.3 4.2 + - - +
153A MET* 3.0 34.7 + - + +
233A ALA* 3.7 28.6 - - + +
255A TYR* 6.1 0.2 - - - -
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Residues in contact with ASP 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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146A LYS* 2.8 55.0 + - - +
147A TYR* 3.8 6.6 - - - +
148A PHE 3.3 0.2 - - - -
149A ALA* 1.3 76.4 - - - +
151A LEU* 1.3 65.9 + - + +
153A MET* 3.8 7.8 - - - +
154A ASN* 3.0 41.1 + - - +
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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 TYR* 3.2 46.1 + - + +
148A PHE* 3.2 10.8 + - + +
150A ASP* 1.3 76.8 - - + +
152A ALA* 1.3 62.3 + - - +
154A ASN* 4.0 4.0 - - - +
155A TYR* 3.3 21.8 + - - +
162A PRO* 4.1 35.2 - - + +
163A LYS 5.6 0.2 - - - +
164A VAL* 3.7 31.0 - - + -
231A PRO* 4.8 2.7 - - - +
254A GLN* 3.8 15.0 - - - +
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Residues in contact with ALA 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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119A ALA 5.7 0.8 - - - +
120A ASN* 4.0 5.1 - - - +
148A PHE 3.2 7.7 + - - +
149A ALA 3.6 7.6 - - - +
150A ASP 3.2 0.2 - - - -
151A LEU* 1.3 79.6 - - - +
153A MET* 1.3 61.9 + - - +
155A TYR* 3.2 19.4 + - - +
230A ARG* 5.3 1.9 + - - -
231A PRO* 3.8 17.5 - - + +
232A VAL* 3.4 16.6 - - - +
233A ALA* 3.3 33.4 - - + +
254A GLN* 5.1 0.6 + - - +
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Residues in contact with MET 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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120A ASN* 3.2 73.0 + - + +
121A ARG* 5.5 1.3 - - - +
149A ALA* 3.0 24.0 + - + +
150A ASP* 3.3 10.5 + - - +
152A ALA* 1.3 76.6 - - - +
154A ASN* 1.3 64.9 + - - +
155A TYR 3.5 5.2 + - - +
156A LYS* 4.5 5.4 + - - -
233A ALA* 4.2 15.7 - - + -
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Residues in contact with ASN 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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150A ASP* 3.0 34.0 + - - +
151A LEU* 4.2 5.0 - - - +
153A MET* 1.3 79.0 - - - +
155A TYR* 1.3 63.7 + - - +
156A LYS* 3.5 13.1 + - - +
159A ASP* 4.1 4.7 - - - +
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Residues in contact with TYR 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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120A ASN* 5.3 0.9 - - - +
151A LEU 3.3 13.4 + - - +
152A ALA 3.2 15.6 + - - +
153A MET 4.0 5.0 - - - +
154A ASN* 1.3 79.2 - - - +
156A LYS* 1.3 81.2 + - - +
157A HIS* 3.7 14.0 + - + -
158A GLY 4.2 2.4 + - - -
159A ASP* 3.3 43.4 + - + -
161A ILE* 4.0 17.2 - - + +
162A PRO* 4.3 13.5 - - + -
229A ILE 4.3 9.9 + - - -
230A ARG* 3.4 47.9 + - + +
231A PRO* 3.5 30.7 - - + -
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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