Contacts of the helix formed by residues 124 - 135 (chain B) in PDB entry 1P45
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 ALA 124 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B HIS* 4.8 1.0 + - - -
120B ILE* 2.5 43.9 + - + +
122B ILE 3.6 3.0 + - - -
123B SER* 1.3 76.5 - - - +
125B TYR* 1.4 65.8 + - - +
126B SER* 3.1 2.3 + - - -
127B TYR* 3.1 19.8 + - - +
128B ALA 4.0 0.5 + - - -
164B ALA 4.0 15.5 - - - +
167B ALA* 4.4 9.2 - - + -
168B LEU* 4.4 11.4 - - - +
171B VAL* 4.0 15.3 - - + +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE 4.5 8.8 + - - -
111A ALA 2.4 30.1 + - - -
112A PRO* 3.9 1.2 - - - +
113A TYR* 3.5 48.5 + + + -
116A VAL* 4.1 6.3 - - + -
160A TRP* 3.6 39.8 - + - -
120B ILE* 3.0 4.9 + - - +
121B HIS* 3.3 29.4 - + - +
124B ALA* 1.4 77.6 - - - +
126B SER* 1.3 54.0 + - - +
128B ALA* 2.7 31.5 + - + +
129B SER* 3.1 42.1 + - - -
132B LYS* 6.0 0.7 - - - +
171B VAL* 4.8 0.8 - - - +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 3.2 32.6 - - - +
93B HIS* 3.6 11.8 + - - -
95B ILE* 5.5 0.4 - - - -
121B HIS* 3.0 2.5 + - - -
122B ILE 2.3 36.4 + - - -
124B ALA 3.1 0.5 + - - -
125B TYR* 1.3 75.5 - - - +
127B TYR* 1.3 61.1 + - - +
128B ALA 3.0 0.2 - - - -
129B SER* 3.4 11.9 - - - -
130B MET* 2.7 33.0 + - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 3.0 38.6 + + + +
124B ALA 3.1 13.2 + - - +
126B SER* 1.3 78.2 - - - +
128B ALA* 1.3 56.0 + - - +
130B MET* 3.7 2.9 - - + +
131B ALA* 3.1 23.7 + - - +
144B ILE* 3.4 29.1 + - + +
145B VAL 3.9 0.9 - - - -
146B GLY* 3.6 24.7 - - - -
168B LEU* 4.1 17.3 - - + -
171B VAL* 4.0 16.8 - - + -
172B ASN* 3.5 22.3 + - + -
175B VAL* 4.1 13.0 - - + -
186B SER* 2.6 30.2 + - - -
187B ASN 3.6 11.3 + - - -
188B LEU* 4.1 4.3 - - + -
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.2 0.7 - - + -
109A PHE* 3.3 18.8 - - + -
160A TRP* 4.1 28.3 - - + -
124B ALA 4.0 0.2 + - - -
125B TYR* 2.7 20.6 + - + +
127B TYR* 1.3 72.6 - - - +
129B SER* 1.3 58.7 + - - +
130B MET 3.2 0.2 - - - -
131B ALA 3.2 0.3 + - - -
132B LYS* 2.8 24.7 + - - +
171B VAL* 4.1 4.7 - - + -
175B VAL* 3.9 22.9 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.7 4.4 + - - +
71B LEU* 3.8 34.1 - - - +
125B TYR* 3.1 28.2 + - - -
126B SER* 3.4 20.1 - - - -
128B ALA* 1.3 74.7 - - - +
130B MET* 1.3 65.7 + - - +
131B ALA 2.9 0.7 + - - -
132B LYS* 3.0 14.4 + - - +
133B ALA* 2.8 25.6 + - - +
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Residues in contact with MET 130 (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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11B LEU* 5.1 2.7 - - + -
13B SER* 4.1 13.5 - - - -
63B LEU* 4.3 20.6 - - + -
65B VAL* 4.7 6.7 - - + +
71B LEU* 4.6 6.6 - - + +
74B LEU* 4.8 5.6 - - + -
91B VAL* 3.5 29.6 - - + +
92B VAL 3.6 18.8 - - - +
93B HIS* 3.6 22.0 - - + -
95B ILE* 4.5 10.1 - - - -
126B SER 2.7 24.5 + - - +
127B TYR* 3.7 5.4 - - + +
129B SER* 1.3 75.0 - - - +
131B ALA* 1.3 58.5 + - - +
133B ALA* 3.9 1.1 + - - -
134B LEU* 3.3 39.7 + - + +
144B ILE* 6.0 1.8 - - + -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.8 7.6 - - + -
127B TYR 3.1 15.5 + - - +
128B ALA 3.2 2.0 + - - +
129B SER 3.1 0.6 - - - -
130B MET* 1.3 75.3 - - - +
132B LYS* 1.3 65.0 + - - +
134B LEU* 4.4 0.4 - - - +
135B LEU* 3.0 41.0 + - + +
144B ILE* 4.1 17.9 - - + +
175B VAL* 3.6 31.4 - - + -
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Residues in contact with LYS 132 (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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109A PHE* 3.2 53.1 + - + +
110A ASP* 3.1 24.8 + - - +
68B GLU* 5.6 8.1 - - - -
125B TYR* 6.0 0.7 - - - +
128B ALA 2.8 21.3 + - - +
129B SER* 3.5 11.9 - - - +
131B ALA* 1.3 72.7 - - - +
133B ALA* 1.3 63.4 + - - +
135B LEU* 5.1 0.2 - - - -
136B PRO* 3.4 17.2 - - - +
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Residues in contact with ALA 133 (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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71B LEU* 3.7 31.0 - - + +
74B LEU* 3.9 26.0 - - + -
75B ALA* 3.7 20.6 - - + +
129B SER 2.8 18.0 + - - +
130B MET 4.3 0.9 - - - +
132B LYS* 1.3 76.0 - - + +
134B LEU* 1.3 58.3 + - - +
136B PRO* 3.2 14.3 - - - +
137B ILE 4.8 0.5 + - - -
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Residues in contact with LEU 134 (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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11B LEU* 4.3 14.6 - - + -
74B LEU* 3.8 29.8 - - + -
78B VAL* 4.4 11.2 - - + -
88B LEU* 4.3 10.2 - - + +
91B VAL* 4.0 32.5 - - + -
130B MET* 3.3 36.5 + - + +
131B ALA* 3.2 3.7 + - - -
133B ALA* 1.3 79.5 - - - +
135B LEU* 1.3 66.5 + - - +
136B PRO* 3.2 2.7 - - - -
137B ILE* 3.2 34.1 + - + +
138B MET* 3.1 19.8 - - - +
144B ILE* 6.1 0.7 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE* 3.6 31.0 - - + -
131B ALA* 3.0 30.4 + - + +
132B LYS* 5.4 0.2 - - - -
134B LEU* 1.3 76.5 - - - +
136B PRO* 1.3 68.5 - - + +
138B MET* 3.1 19.5 + - - +
144B ILE* 4.1 8.1 - - + -
179B ALA* 3.9 37.5 - - + +
182B TYR* 3.4 38.6 - - + -
184B VAL* 3.9 30.5 - - + -
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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