Contacts of the helix formed by residues 153 - 167 (chain A) in PDB entry 3HM5
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 THR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A TYR* 3.5 2.0 - - - -
152A TRP* 1.3 75.0 - - - +
154A LYS* 1.3 63.5 + - - +
155A ALA* 3.5 11.9 + - + +
156A GLU* 2.8 35.9 + - - +
157A THR* 2.9 26.7 + - - -
183A PHE* 4.2 6.6 - - + -
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Residues in contact with LYS 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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138A TYR* 4.3 7.2 - - - -
140A GLU* 4.5 19.4 - - - +
143A TYR* 3.4 57.2 + - + -
148A HIS* 5.6 2.4 - - + -
153A THR* 1.3 70.4 - - - +
155A ALA* 1.3 60.9 + - - +
157A THR* 3.2 0.5 + - - -
158A ASP* 2.8 69.5 + - - +
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Residues in contact with ALA 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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153A THR* 3.2 11.0 + - + +
154A LYS* 1.3 79.2 - - - +
156A GLU* 1.3 61.9 + - - +
158A ASP* 3.4 9.2 + - - +
159A HIS* 3.0 22.5 + - - +
182A GLN* 5.9 0.7 - - - +
183A PHE* 4.1 15.3 - - + -
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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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151A ALA 4.4 0.2 - - - +
152A TRP* 3.4 16.7 - - + -
153A THR* 2.8 24.7 + - - +
155A ALA* 1.3 70.5 - - - +
157A THR* 1.3 62.5 + - - +
159A HIS* 3.2 4.7 + - - +
160A LEU* 2.9 28.1 + - - +
178A TYR* 2.6 34.1 + - + +
183A PHE* 3.6 41.8 - - + +
184A LYS* 5.0 2.2 + - - +
186A ARG* 2.8 42.7 + - - +
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Residues in contact with THR 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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138A TYR* 3.3 15.3 - - + +
143A TYR* 3.2 15.6 + - + -
152A TRP* 3.6 11.0 - - - -
153A THR 2.9 18.0 + - - -
154A LYS 3.7 3.4 - - - -
156A GLU* 1.3 77.2 - - - +
158A ASP* 1.3 61.5 + - - +
160A LEU* 3.2 3.8 + - + +
161A PHE* 3.0 27.5 + - + -
194A ARG* 3.0 26.5 + - + +
198A ILE* 3.3 33.7 - - + -
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 2.6 32.1 + - - -
154A LYS* 2.8 57.6 + - - +
155A ALA* 3.5 8.3 - - - +
157A THR* 1.3 71.6 - - - +
159A HIS* 1.3 52.4 + - - +
161A PHE* 3.3 3.8 + - - +
162A ASP* 2.8 35.6 + - - +
165A ARG* 4.9 1.4 + - - -
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Residues in contact with HIS 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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155A ALA 3.0 14.3 + - - +
156A GLU 3.2 8.3 - - - +
158A ASP* 1.3 72.7 - - - +
160A LEU* 1.3 65.0 + - - +
162A ASP* 3.3 11.7 + - - +
163A LEU* 2.9 56.4 + - + +
166A ARG* 5.7 1.3 - - - -
177A ARG 4.5 3.1 - - - -
178A TYR* 4.0 17.9 - + - -
179A ASP* 2.9 36.3 + - + +
183A PHE* 3.6 32.1 - + + -
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Residues in contact with LEU 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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152A TRP* 4.0 8.1 - - + -
156A GLU 2.9 15.8 + - - +
157A THR* 3.2 8.0 + - - +
159A HIS* 1.3 73.5 - - - +
161A PHE* 1.3 73.3 + - + +
163A LEU* 3.4 3.4 + - - +
164A SER* 2.8 39.8 + - - +
171A PHE* 4.5 4.9 - - + -
174A ILE* 4.0 20.6 - - + -
178A TYR* 4.2 18.4 - - + +
191A LEU* 3.9 32.5 - - + +
194A ARG* 3.8 30.5 - - + -
195A TYR* 4.0 8.3 - - + +
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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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135A VAL* 3.5 11.7 - - + +
136A PRO* 3.5 35.0 - - + -
138A TYR* 3.9 22.9 - + + +
157A THR* 3.0 22.3 + - + +
158A ASP* 3.8 4.3 - - - +
160A LEU* 1.3 81.7 - - + +
162A ASP* 1.3 65.9 + - - +
164A SER* 3.3 6.4 + - - -
165A ARG* 3.0 43.0 + - - +
195A TYR* 3.5 39.3 - + - -
198A ILE* 3.5 47.8 - - + -
199A CYS* 5.2 0.4 - - - -
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Residues in contact with ASP 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 ASP 2.8 17.0 + - - +
159A HIS* 3.3 12.8 + - - +
161A PHE* 1.3 76.5 - - - +
163A LEU* 1.3 62.8 + - - +
165A ARG* 3.2 18.3 + - - +
166A ARG* 3.0 67.0 + - - +
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Residues in contact with LEU 163 (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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159A HIS* 2.9 51.4 + - + +
160A LEU* 3.8 3.6 - - - +
162A ASP* 1.3 76.2 - - - +
164A SER* 1.3 57.4 + - - +
166A ARG* 3.7 19.5 - - - +
167A PHE* 2.9 63.4 + - + +
174A ILE* 3.8 26.4 - - + +
177A ARG* 4.3 11.2 - - + +
178A TYR* 3.7 26.9 - - + +
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Residues in contact with SER 164 (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 VAL* 3.7 11.1 - - - +
160A LEU* 2.8 28.1 + - - +
161A PHE 3.4 6.5 - - - -
162A ASP 3.2 0.2 - - - -
163A LEU* 1.3 76.1 - - - +
165A ARG* 1.3 60.4 + - - +
168A ASP* 3.3 3.3 + - - -
169A LEU* 3.0 41.2 + - - +
171A PHE* 4.5 0.7 - - - -
174A ILE* 3.6 21.0 - - - +
195A TYR* 3.8 25.5 - - - -
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Residues in contact with ARG 165 (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 CA 2.5 27.4 - - - -
135A VAL* 3.8 22.8 + - + +
136A PRO 3.1 24.9 + - - -
137A VAL* 3.7 27.7 - - - +
138A TYR* 5.2 1.8 - - - +
158A ASP 4.9 1.2 + - - -
161A PHE* 3.0 46.1 + - - +
162A ASP* 3.2 18.3 + - - +
164A SER* 1.3 75.9 - - - +
166A ARG* 1.3 65.5 + - + +
167A PHE 3.3 0.7 + - - -
168A ASP* 3.5 2.4 - - - +
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Residues in contact with ARG 166 (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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159A HIS* 5.7 2.0 - - - -
162A ASP* 3.0 50.1 + - - +
163A LEU* 3.7 18.5 - - - +
165A ARG* 1.3 78.8 - - + +
167A PHE* 1.3 96.7 + - + +
168A ASP* 3.5 8.8 + - - +
177A ARG* 4.4 10.7 - - - +
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Residues in contact with PHE 167 (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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163A LEU* 2.9 52.1 + - + +
164A SER 4.1 0.7 - - - -
166A ARG* 1.3 109.5 - - + +
168A ASP* 1.3 69.9 + - - +
169A LEU 3.2 2.9 - - - -
170A ARG* 3.0 31.7 + - - +
173A VAL* 3.6 32.8 - - + -
174A ILE* 4.4 9.0 - - + -
177A ARG* 4.1 35.2 - - + -
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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