Contacts of the helix formed by residues 157 - 167 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.9 8.9 - - + -
134B HIS* 3.4 54.3 + + + -
153B VAL* 3.7 5.2 - - + +
154B SER* 2.9 23.9 + - - +
156B GLU* 1.3 99.9 + - + +
158B LEU* 1.3 61.2 + - - -
159B GLU 3.6 0.7 - - - -
160B GLY* 3.6 4.6 + - - +
161B ALA* 3.2 25.8 + - - +
887B GLN* 5.9 5.5 - - - +
891B ILE* 5.8 0.7 - - + -
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER* 3.7 26.9 - - - +
87B SER 5.2 1.3 - - - +
151B PHE* 4.8 9.2 - - + -
153B VAL* 4.0 9.2 - - + -
154B SER 3.8 1.6 + - - -
155B HIS 3.7 13.5 + - - +
156B GLU 3.1 3.2 - - - +
157B HIS* 1.3 73.5 - - - +
159B GLU* 1.3 60.5 + - - +
160B GLY 3.0 0.5 + - - -
161B ALA* 3.1 2.1 + - - +
162B LEU* 2.7 58.8 + - + -
258B VAL* 4.1 11.0 - - + -
259B LEU 4.2 2.9 - - - +
260B GLY* 3.9 8.3 - - - -
262B GLU* 3.4 31.4 - - - +
267B LEU* 4.4 10.8 - - + -
270B LEU* 4.2 7.6 - - + -
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLU 4.4 6.1 + - - +
157B HIS 3.6 0.4 - - - -
158B LEU* 1.3 77.6 - - - +
160B GLY* 1.3 64.0 + - - +
162B LEU* 4.0 2.3 - - - +
163B ASP* 3.1 27.5 + - - +
262B GLU* 5.6 0.4 + - - -
270B LEU* 3.3 37.9 - - + +
273B LYS* 3.1 31.4 + - - +
274B LEU* 4.4 7.8 - - - +
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PHE* 3.7 9.2 - - - -
157B HIS* 3.6 4.6 + - - +
158B LEU 3.1 1.0 - - - -
159B GLU* 1.3 79.7 - - - +
161B ALA* 1.3 63.7 + - - +
163B ASP* 3.4 5.5 + - - +
164B ARG* 2.7 47.3 + - - +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TYR* 4.3 4.8 - - - -
130B PHE* 3.2 20.8 - - + -
131B LEU* 3.8 16.6 - - + -
151B PHE* 3.5 26.5 - - + -
153B VAL* 4.0 3.8 - - + -
157B HIS 3.2 16.7 + - - +
158B LEU 3.1 1.6 + - - +
160B GLY* 1.3 73.6 - - - +
162B LEU* 1.3 63.3 + - - +
163B ASP 3.3 0.3 + - - -
164B ARG* 3.4 6.0 + - - +
165B PHE* 3.1 22.0 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 4.0 19.1 - - + -
151B PHE* 3.9 5.9 - - + -
158B LEU* 2.7 41.7 + - + +
159B GLU* 4.1 3.6 - - - +
161B ALA* 1.3 72.7 - - - +
163B ASP* 1.3 56.7 + - - +
165B PHE* 3.4 15.2 - - + +
166B ALA* 2.9 28.4 + - - +
258B VAL* 4.2 18.2 - - + -
270B LEU* 4.2 23.6 - - + +
271B VAL* 5.2 1.3 - - + -
274B LEU* 3.9 10.8 - - + -
275B PHE* 3.7 32.5 - - + -
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 3.1 23.3 + - - -
121B TYR* 2.6 29.7 + - - +
159B GLU* 3.1 21.7 + - + +
160B GLY* 3.5 7.6 - - - +
162B LEU* 1.3 76.8 - - - +
164B ARG* 1.3 63.1 + - - +
166B ALA* 3.1 14.3 + - - +
167B GLN* 3.2 20.9 + - - +
274B LEU* 3.1 33.0 - - + +
277B GLU* 5.5 0.3 - - - +
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Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR* 4.8 0.9 + - - +
121B TYR* 3.7 47.3 + - + +
126B GLU* 2.9 37.6 + - - +
127B TYR* 3.9 16.6 - - + +
130B PHE* 3.4 46.4 - - - -
160B GLY* 2.7 44.1 + - - +
161B ALA* 3.7 5.8 - - - +
163B ASP* 1.3 74.3 - - - +
165B PHE* 1.3 62.1 + - - +
167B GLN* 3.2 16.8 - - - +
168B PHE* 3.4 14.0 - - - -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA* 4.6 1.1 - - + -
89B ALA* 4.0 7.4 - - - -
90B LEU* 3.6 36.8 - - + -
127B TYR* 3.4 31.8 - + + -
138B SER* 5.8 0.2 - - - -
149B TYR* 3.7 32.3 - - + -
150B TYR* 4.2 1.3 - - - -
151B PHE* 3.7 15.9 - + + -
161B ALA 3.1 14.5 + - - +
162B LEU* 3.4 27.1 - - + +
164B ARG* 1.3 72.2 - - - +
166B ALA* 1.3 58.5 + - - +
167B GLN 3.0 4.0 - - - -
168B PHE* 2.9 41.3 + + - +
169B PHE* 3.5 21.6 - + - -
256B VAL* 5.9 0.9 - - + -
275B PHE* 4.2 9.9 - + - -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LEU 2.9 17.0 + - - +
163B ASP* 3.1 6.9 + - - +
165B PHE* 1.3 75.8 - - - +
167B GLN* 1.3 62.2 + - - +
169B PHE* 3.3 16.8 + - - +
170B LEU* 3.4 17.0 - - - +
274B LEU* 3.6 30.1 - - + +
275B PHE* 3.7 27.2 - - + -
277B GLU* 5.1 2.9 - - - +
278B VAL* 5.4 1.0 - - - +
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Residues in contact with GLN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B THR* 3.5 23.9 + - + +
119B LYS* 4.8 0.3 - - - +
120B LYS* 3.3 42.0 + - - +
121B TYR* 3.7 22.4 - - + -
163B ASP* 3.2 21.2 + - - +
164B ARG 3.2 12.3 - - - +
165B PHE 2.9 0.4 + - - -
166B ALA* 1.3 73.7 - - - +
168B PHE* 1.3 54.3 + - - +
169B PHE 2.9 5.6 - - - -
170B LEU* 2.9 41.5 + - - +
171B SER* 3.2 23.6 + - - -
277B GLU* 4.6 4.8 + - - -
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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