Contacts of the helix formed by residues 143 - 149 (chain A) in PDB entry 2PHA
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 GLN 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A VAL* 4.5 3.9 - - - +
128A ASP 3.4 4.9 - - - -
130A ASN* 3.3 23.3 - - + +
131A THR 4.2 0.2 - - - -
132A PRO* 3.6 27.7 - - - +
135A THR* 3.7 21.4 + - - +
138A GLY* 3.3 29.1 + - - -
139A ASN 3.4 10.8 + - - +
140A LEU* 3.4 27.7 - - + +
142A GLY* 1.3 84.1 - - - +
144A PRO* 1.4 67.4 - - - +
146A SER* 2.9 25.6 + - - -
147A PHE* 3.5 12.9 - - + -
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Residues in contact with PRO 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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101A HIS 3.7 22.7 - - - +
102A SER* 4.5 0.7 - - - -
104A ALA* 4.2 3.8 - - + -
105A ILE* 3.5 27.7 - - + +
122A TRP* 3.9 15.7 - - + -
128A ASP* 3.7 16.6 - - + +
140A LEU 3.1 15.6 - - - +
141A HIS* 3.5 10.1 - - - +
142A GLY 3.6 1.3 - - - -
143A GLN* 1.4 89.9 - - - +
145A VAL* 1.3 63.7 + - - +
147A PHE* 3.0 15.4 + - - +
148A LEU* 3.3 17.2 + - + +
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Residues in contact with VAL 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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122A TRP* 3.5 36.1 - - + -
127A THR 3.5 14.1 - - - +
128A ASP 3.1 20.2 + - - +
129A ILE* 4.0 5.2 - - + -
144A PRO* 1.3 71.7 - - - +
146A SER* 1.3 57.1 + - - +
148A LEU* 3.3 10.5 + - + +
149A LEU* 3.1 49.7 + - + +
169A ILE* 5.6 1.1 - - + -
174A ILE* 4.2 14.8 - - + -
176A TYR* 3.3 20.4 - - + +
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Residues in contact with SER 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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128A ASP 4.1 1.2 + - - -
129A ILE* 3.7 14.5 - - - +
130A ASN 2.8 29.8 + - - -
131A THR* 3.7 7.2 - - - -
143A GLN 2.9 10.2 + - - -
145A VAL* 1.3 78.5 - - - +
147A PHE* 1.3 67.5 + - - +
148A LEU 3.6 0.2 + - - -
149A LEU 4.1 4.9 + - - +
152A LEU* 4.0 27.2 - - - +
156A ILE* 3.6 27.5 - - - +
167A PRO* 5.8 0.3 - - - +
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Residues in contact with PHE 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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105A ILE* 3.8 27.4 - - + -
132A PRO* 3.8 10.1 - - + -
140A LEU* 3.5 31.2 - - + -
143A GLN* 3.5 25.6 - - + -
144A PRO 3.0 8.0 + - - +
146A SER* 1.3 86.2 + - - +
148A LEU* 1.3 61.5 + - - +
156A ILE* 3.9 15.9 - - + -
157A PRO 5.1 0.2 - - - -
159A VAL* 3.5 34.1 - - + -
162A PHE* 3.7 30.5 - + + -
165A VAL* 3.6 23.8 - - + +
167A PRO* 3.8 15.0 - - - +
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Residues in contact with LEU 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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104A ALA* 4.1 3.1 - - + +
105A ILE* 3.4 43.5 - - + +
108A ILE* 3.5 36.8 - - + -
109A SER* 3.4 12.3 - - - +
122A TRP* 4.7 4.7 - - + -
144A PRO 3.3 18.3 + - - +
145A VAL* 3.8 9.6 - - + +
146A SER 3.3 0.6 - - - -
147A PHE* 1.3 80.6 - - - +
149A LEU* 1.3 57.6 + - - +
165A VAL* 5.3 1.8 - - + -
166A THR 5.8 0.4 - - - +
167A PRO* 3.3 4.0 - - - +
168A CYS* 2.9 39.1 + - - +
169A ILE* 3.1 24.1 - - + +
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Residues in contact with LEU 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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129A ILE* 3.7 30.7 - - + -
145A VAL* 3.1 24.9 + - + +
146A SER 4.1 3.0 + - - +
147A PHE 3.7 0.4 - - - -
148A LEU* 1.3 75.5 - - - +
150A LYS* 1.3 65.1 + - - +
151A GLU* 4.3 4.7 - - - +
152A LEU* 3.4 26.5 + - + +
153A LYS 3.9 2.4 + - - -
167A PRO* 3.5 9.3 - - - +
169A ILE* 3.0 32.8 - - + +
170A SER 3.5 3.8 - - - +
171A ALA* 3.4 23.8 - - - +
174A ILE* 4.4 7.9 - - + -
193A LEU* 3.7 19.3 - - + -
195A ILE* 4.0 9.0 - - + -
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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