Contacts of the helix formed by residues 157 - 167 (chain A) in PDB entry 3H44
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 HIS 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A PHE* 4.2 10.2 - - + -
134A HIS* 3.2 42.3 + + + -
153A VAL* 3.8 20.2 - - + -
154A SER* 3.1 24.5 + - - -
156A GLU* 1.3 92.8 + - + +
158A LEU* 1.3 67.1 + - - +
159A GLU 3.4 2.7 - - - +
160A GLY 3.5 3.8 + - - +
161A ALA* 3.0 25.3 + - - +
887A GLN* 6.2 1.8 - - - +
891A ILE* 5.8 2.1 - - + +
458B GLU* 6.4 2.0 - - + -
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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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86A SER* 3.6 26.2 - - - +
87A SER 4.3 13.2 - - - +
88A ALA* 5.1 0.4 - - + -
151A PHE* 4.4 17.5 - - + -
153A VAL* 3.9 7.2 - - + +
155A HIS 3.9 11.4 + - - +
156A GLU 3.6 1.2 - - - -
157A HIS* 1.3 79.2 - - - +
159A GLU* 1.3 53.4 + - - +
161A ALA* 3.5 1.2 - - - +
162A LEU* 2.6 41.8 + - + +
258A VAL* 4.0 24.2 - - + -
259A LEU 4.3 3.8 - - - +
262A GLU* 4.2 25.1 - - - +
267A LEU* 4.2 7.0 - - + -
270A LEU* 4.1 18.8 - - + -
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Residues in contact with GLU 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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157A HIS 3.4 0.4 - - - -
158A LEU* 1.3 80.4 - - - +
160A GLY* 1.3 55.7 + - - +
162A LEU* 3.0 5.9 + - - +
163A ASP* 2.6 40.3 + - + +
262A GLU* 5.6 0.2 + - - -
270A LEU* 3.7 26.1 - - + +
273A LYS* 2.6 36.7 + - - +
274A LEU* 4.6 5.2 - - + +
408B GLU* 5.9 0.9 - - - +
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Residues in contact with GLY 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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130A PHE* 3.5 11.0 - - - -
157A HIS* 3.5 4.4 + - - +
158A LEU 3.4 0.4 - - - -
159A GLU* 1.3 78.8 - - - +
161A ALA* 1.3 64.2 + - - +
163A ASP* 3.4 2.0 + - - +
164A ARG* 2.8 37.9 + - - +
408B GLU* 3.3 24.8 + - - -
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Residues in contact with ALA 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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127A TYR* 4.6 2.9 - - - -
130A PHE* 3.1 19.2 - - + -
131A LEU* 3.9 15.0 - - + -
151A PHE* 3.5 28.0 - - + -
153A VAL* 3.9 5.2 - - + -
157A HIS 3.0 18.2 + - - +
158A LEU 3.5 2.5 - - - +
160A GLY* 1.3 76.4 - - - +
162A LEU* 1.3 65.2 + - - +
164A ARG* 3.3 4.1 + - - +
165A PHE* 3.0 21.0 + - - +
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Residues in contact with LEU 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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88A ALA* 3.9 21.8 - - + -
151A PHE* 3.9 4.9 - - + -
158A LEU* 2.6 25.2 + - + +
159A GLU 3.6 3.4 - - - +
161A ALA* 1.3 72.6 - - - +
163A ASP* 1.3 57.1 + - - +
165A PHE* 3.4 24.2 - - + +
166A ALA* 2.9 28.9 + - - +
258A VAL* 4.3 19.5 - - + -
270A LEU* 3.0 35.4 - - + -
271A VAL* 4.9 1.8 - - + -
274A LEU* 3.6 13.2 - - + -
275A PHE* 3.9 19.7 - - + -
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Residues in contact with ASP 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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120A LYS* 3.2 25.0 + - - -
121A TYR* 2.3 35.1 + - - +
159A GLU* 2.6 23.9 + - + +
160A GLY* 3.8 6.1 - - - +
161A ALA 3.2 0.2 - - - -
162A LEU* 1.3 70.7 - - - +
164A ARG* 1.3 68.0 + - - +
165A PHE 3.0 1.2 + - - -
166A ALA* 3.3 4.2 + - - +
167A GLN* 3.0 25.1 + - - -
274A LEU* 3.1 32.0 - - + +
408B GLU* 4.4 8.7 + - - +
409B TRP 4.5 0.9 + - - -
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Residues in contact with ARG 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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118A THR* 4.9 1.0 + - - -
121A TYR* 3.7 38.3 + - + +
126A GLU* 2.7 38.0 + - + +
127A TYR* 4.2 16.8 - - + +
130A PHE* 3.4 37.0 - - - -
160A GLY 2.8 37.1 + - - +
161A ALA 3.7 6.3 - - - +
163A ASP* 1.3 76.2 - - - +
165A PHE* 1.3 60.7 + - - +
167A GLN* 3.5 13.2 + - - +
168A PHE* 3.6 15.9 - - - -
408B GLU* 2.9 40.5 + - - +
412B GLN* 3.8 14.6 + - - -
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Residues in contact with PHE 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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88A ALA* 4.9 2.2 - - + -
89A ALA* 4.3 7.0 - - - -
90A LEU* 3.9 22.2 - - + -
115A PHE* 6.5 0.2 - + - -
127A TYR* 3.6 26.9 - + + -
149A TYR* 3.6 40.4 - - + -
150A TYR 4.4 0.4 - - - -
151A PHE* 3.7 22.9 - + + -
161A ALA 3.0 16.9 + - - +
162A LEU* 3.4 22.0 - - + +
163A ASP 3.0 0.6 - - - -
164A ARG* 1.3 74.7 - - - +
166A ALA* 1.3 70.0 + - - +
167A GLN 3.0 2.1 + - - -
168A PHE* 3.1 35.0 + + - +
169A PHE* 3.5 19.3 - + - -
256A VAL* 5.7 0.9 - - + -
275A PHE* 4.4 10.8 - + - -
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Residues in contact with ALA 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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162A LEU 2.9 16.2 + - - +
163A ASP 3.3 4.9 + - - +
165A PHE* 1.3 76.4 - - - +
167A GLN* 1.3 71.2 + - - +
169A PHE* 2.8 28.9 + - - +
170A LEU* 3.7 9.5 + - + +
274A LEU* 3.6 29.6 - - + +
275A PHE* 3.9 21.5 - - + -
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Residues in contact with GLN 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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118A THR* 3.3 30.4 - - + +
120A LYS* 3.3 52.5 + - + +
121A TYR* 3.9 11.2 - - + -
163A ASP* 3.0 28.8 + - - +
164A ARG 3.6 4.9 - - - +
165A PHE 3.0 1.4 - - - -
166A ALA* 1.3 81.6 - - - +
168A PHE* 1.3 61.9 + - - +
169A PHE 2.9 2.2 + - - -
170A LEU* 3.0 37.6 + - + +
171A SER* 3.0 18.4 + - - +
274A LEU* 5.2 1.8 + - - +
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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