Contacts of the helix formed by residues 155 - 169 (chain A) in PDB entry 1P84
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 ASP 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASP 4.2 0.6 + - - -
151A PHE* 3.0 38.2 + - + +
154A ASN* 1.3 68.9 - - - +
156A HIS* 1.3 57.4 + - - +
157A PRO* 3.7 9.2 - - - +
158A ASN* 2.7 46.4 + - - +
159A ARG* 2.8 32.0 + - - +
179A ARG* 5.3 1.2 + - - -
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Residues in contact with HIS 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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153A ASP 3.6 17.5 + - - -
154A ASN* 2.9 30.0 + - - -
155A ASP* 1.3 68.2 - - - +
157A PRO* 1.3 75.7 - - + +
159A ARG* 3.1 36.7 + - - +
160A VAL* 2.8 29.4 + - - +
256A LEU* 3.5 34.2 - - + +
257A PRO* 6.0 0.4 - - + -
260A TRP* 3.7 39.3 - + + -
436A THR* 4.2 4.3 - - + -
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Residues in contact with PRO 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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154A ASN 5.1 0.4 - - - +
155A ASP* 3.7 9.6 - - - +
156A HIS* 1.3 93.8 - - + +
158A ASN* 1.3 61.4 + - - +
160A VAL* 3.4 6.4 + - + +
161A LEU* 3.1 25.8 + - - +
260A TRP* 3.6 29.8 - - + +
262A SER* 4.9 2.1 + - - -
331A SER* 6.1 0.3 - - - -
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Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.5 14.5 - - + -
155A ASP* 2.7 40.3 + - - +
156A HIS 3.3 0.2 - - - -
157A PRO* 1.3 79.2 - - - +
159A ARG* 1.3 57.5 + - - +
161A LEU* 3.3 12.3 + - - +
162A GLU* 2.8 36.0 + - - +
179A ARG* 5.2 6.6 + - - +
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Residues in contact with ARG 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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151A PHE* 3.8 16.5 - - + +
152A GLU* 3.2 57.2 + - - +
155A ASP 2.8 18.8 + - - +
156A HIS* 3.1 35.9 + - - +
158A ASN* 1.3 77.0 - - - +
160A VAL* 1.3 57.2 + - + +
162A GLU* 3.6 2.8 - - - +
163A HIS* 2.9 42.3 + - - +
251A LEU* 4.2 22.8 + - + +
253A ASP* 5.4 6.1 + - - +
256A LEU* 4.3 3.2 - - - +
436A THR* 3.3 30.4 + - - +
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Residues in contact with VAL 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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156A HIS 2.8 19.7 + - - +
157A PRO* 3.7 5.4 - - + +
159A ARG* 1.3 76.5 - - + +
161A LEU* 1.3 59.2 + - - +
163A HIS* 3.1 7.6 + - - +
164A LEU* 2.9 26.7 + - - +
251A LEU* 5.5 3.1 - - + -
260A TRP* 3.8 17.7 - - + +
261A ILE 4.3 1.1 - - - -
262A SER* 3.5 22.9 - - - +
434A ALA* 3.4 27.8 - - - +
435A GLY* 4.1 3.4 - - - +
436A THR* 3.4 33.9 - - + +
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Residues in contact with LEU 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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157A PRO 3.1 16.7 + - - +
158A ASN* 3.3 14.1 + - - +
160A VAL* 1.3 76.4 - - - +
162A GLU* 1.3 63.8 + - - +
164A LEU* 3.2 35.8 + - + +
165A HIS* 3.0 33.3 + - + -
262A SER* 4.1 10.1 + - - +
318A PHE* 3.9 27.4 - - + -
320A LEU* 4.7 13.7 - - + -
331A SER* 4.1 3.8 - - - +
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Residues in contact with GLU 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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99A ARG* 2.9 36.5 + - - -
151A PHE* 4.7 7.2 - - + -
158A ASN 2.8 18.5 + - - +
159A ARG* 3.6 6.7 - - - +
161A LEU* 1.3 76.1 - - - +
163A HIS* 1.3 61.1 + - - +
165A HIS* 3.3 10.7 + - - +
166A SER* 3.1 18.2 + - - -
175A SER 5.2 0.5 - - - +
177A PRO* 3.7 24.7 - - + +
178A THR* 3.3 26.0 + - - -
179A ARG* 3.6 16.5 + - - -
34E TYR* 3.7 15.9 - - + +
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Residues in contact with HIS 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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152A GLU* 3.3 25.1 - - + -
159A ARG* 2.9 30.2 + - + +
160A VAL* 3.6 8.1 - - - +
162A GLU* 1.3 73.6 - - - +
164A LEU* 1.3 64.2 + - - +
166A SER* 3.1 9.1 + - - -
167A THR* 3.0 25.8 + - - +
249A VAL* 3.9 18.3 - - + +
251A LEU* 3.7 30.9 - - + +
434A ALA* 4.3 3.8 - - + -
33E THR* 2.7 43.6 + - - -
34E TYR* 3.5 22.8 - + - -
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Residues in contact with LEU 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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160A VAL 2.9 12.7 + - - +
161A LEU* 3.2 26.4 + - + +
163A HIS* 1.3 76.3 - - - +
165A HIS* 1.3 55.8 + - - +
167A THR* 3.5 2.3 + - + +
168A ALA* 2.9 35.5 + - + +
262A SER* 3.6 35.9 - - - +
263A LEU 4.3 0.7 - - - +
264A ALA* 4.3 20.0 - - + +
318A PHE* 4.4 4.5 - - + -
327A LEU* 4.3 11.0 - - + -
432A ALA* 3.7 38.4 - - + +
433A ILE 4.3 4.0 - - - +
434A ALA* 3.9 8.1 - - + -
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Residues in contact with HIS 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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99A ARG* 3.3 40.2 + - - +
161A LEU* 3.0 33.8 + - + -
162A GLU* 3.3 6.1 + - - +
163A HIS 3.2 0.2 - - - -
164A LEU* 1.3 78.9 - - - +
166A SER* 1.3 64.3 + - - +
168A ALA* 4.4 1.1 - - - -
169A PHE* 3.1 40.2 + + + +
174A LEU 3.7 4.5 - - - +
175A SER* 3.6 4.7 - - - -
320A LEU* 3.7 16.9 - - + +
322A TYR* 2.8 37.1 + + - -
327A LEU* 3.5 25.2 - - + +
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Residues in contact with SER 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 GLU 3.1 5.3 + - - -
163A HIS* 3.1 26.6 + - - -
165A HIS* 1.3 79.4 - - - +
167A THR* 1.3 54.7 + - - +
170A GLN* 3.3 25.8 + - - +
175A SER* 3.5 22.4 + - - -
249A VAL* 5.9 0.4 - - - -
33E THR 4.6 1.6 + - - -
34E TYR* 3.0 42.2 + - - +
36E THR* 3.9 6.4 + - - -
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Residues in contact with THR 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 HIS 3.0 14.9 + - - +
164A LEU* 3.6 9.2 - - + +
166A SER* 1.3 74.6 + - - +
168A ALA* 1.3 69.9 + - - +
169A PHE 3.2 2.1 + - - -
170A GLN* 3.2 24.3 + - - +
245A LEU 4.0 1.2 - - - +
247A SER* 2.5 45.6 + - - +
248A GLU* 3.6 8.9 + - - -
249A VAL* 3.7 27.6 - - + +
432A ALA* 4.9 0.4 - - + -
433A ILE 3.7 15.9 - - - +
36E THR* 4.5 6.4 - - - +
27H TYR* 5.5 2.8 - - - -
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Residues in contact with ALA 168 (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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164A LEU* 2.9 22.1 + - + +
165A HIS* 4.1 2.2 - - - +
167A THR* 1.3 78.5 - - - +
169A PHE* 1.3 60.4 + - + +
170A GLN 3.6 0.2 - - - -
244A PHE* 3.4 19.3 - - + -
245A LEU* 2.9 37.8 + - - +
327A LEU* 4.1 15.5 - - + -
432A ALA* 3.8 21.3 - - + -
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Residues in contact with PHE 169 (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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165A HIS* 3.1 30.9 + + - +
168A ALA* 1.3 78.7 - - + +
170A GLN* 1.3 69.8 + - - +
172A THR* 2.9 25.2 + - + +
174A LEU* 3.4 40.6 - - + -
175A SER* 3.7 7.2 - - - +
242A ALA* 4.8 0.2 - - + -
243A ALA 3.6 24.9 - - - -
244A PHE* 4.5 14.8 - + - -
245A LEU* 6.0 0.7 - - - -
322A TYR* 5.0 2.7 - + - -
325A SER* 3.5 29.4 - - - -
326A GLY* 3.8 14.1 - - - -
327A LEU* 3.7 36.6 - - + -
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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