Contacts of the helix formed by residues 124 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A ILE* 3.0 21.4 + - + +
122A ILE 3.6 0.2 - - - -
123A SER* 1.3 79.8 - - - +
125A TYR* 1.3 65.1 + - - +
126A SER 3.3 1.3 - - - -
127A TYR* 3.3 19.0 + - - +
164A ALA 3.9 11.9 - - - +
167A ALA* 3.9 29.4 - - + -
168A LEU* 3.9 12.6 - - - +
171A VAL* 3.9 15.3 - - + +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL 5.8 1.3 - - - -
120A ILE* 2.9 13.3 + - + +
121A HIS* 3.6 30.1 - + - +
124A ALA* 1.3 72.6 - - - +
126A SER* 1.3 66.4 + - - +
128A ALA* 2.9 16.9 + - + +
129A SER* 3.2 33.8 + - - -
171A VAL* 4.9 0.4 - - - +
109B PHE 4.8 3.1 + - - -
111B ALA 2.4 30.5 + - - -
112B PRO* 3.5 3.2 - - - +
113B TYR* 3.4 47.5 + + + -
116B VAL* 4.5 5.4 - - + -
160B TRP* 3.6 41.0 - + + -
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Residues in contact with SER 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.5 32.7 - - - +
93A HIS* 2.4 37.1 + - - -
95A ILE* 3.9 3.8 - - - +
121A HIS 2.9 10.0 + - - -
122A ILE 2.8 20.2 + - - -
124A ALA 3.3 0.6 - - - -
125A TYR* 1.3 77.6 - - - +
127A TYR* 1.3 55.5 + - - +
128A ALA 3.3 0.2 - - - -
129A SER* 3.2 10.0 + - - -
130A MET* 2.9 32.4 + - - +
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Residues in contact with TYR 127 (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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93A HIS* 3.4 34.0 + + + +
124A ALA 3.3 5.4 + - - +
125A TYR 2.9 1.4 + - - -
126A SER* 1.3 79.8 + - - +
128A ALA* 1.3 60.6 + - - +
130A MET* 4.0 2.4 - - + +
131A ALA* 3.2 20.4 + - - +
144A ILE* 2.9 42.2 + - + +
146A GLY* 3.6 23.1 - - - -
168A LEU* 3.5 28.7 - - + -
171A VAL* 4.0 5.4 - - + -
172A ASN* 4.2 11.0 - - + -
175A VAL* 4.0 24.0 - - + -
186A SER* 2.9 27.9 + - - -
187A ASN 3.6 8.5 + - - -
188A LEU* 4.1 4.9 - - + -
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Residues in contact with ALA 128 (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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125A TYR* 2.9 11.6 + - + +
127A TYR* 1.3 76.5 - - - +
129A SER* 1.3 53.6 - - - +
131A ALA* 2.6 28.2 + - - +
132A LYS* 2.7 18.2 + - - +
171A VAL* 3.9 20.9 - - + +
175A VAL* 4.3 5.6 - - + -
108B PHE* 4.4 1.8 - - + -
109B PHE* 3.9 19.8 - - + -
160B TRP* 4.2 21.3 - - + -
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Residues in contact with SER 129 (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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65A VAL* 4.7 3.0 + - - +
71A LEU* 4.2 28.3 - - - +
125A TYR* 3.2 33.3 + - - -
126A SER* 3.2 17.5 + - - -
128A ALA* 1.3 77.1 - - - +
130A MET* 1.3 65.9 + - - +
132A LYS* 3.3 13.7 + - - +
133A ALA* 3.3 22.5 + - - +
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Residues in contact with MET 130 (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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11A LEU* 4.8 4.7 - - - -
13A SER* 3.9 12.8 - - - +
63A LEU* 4.6 9.9 - - + -
65A VAL* 3.8 17.3 - - + -
71A LEU* 4.3 10.4 - - + +
74A LEU* 5.4 4.0 - - + -
91A VAL* 4.6 9.6 - - + +
92A VAL 4.6 3.4 - - - +
93A HIS* 3.5 39.3 - - + -
95A ILE* 3.7 21.1 - - + -
126A SER 2.9 13.6 + - - +
127A TYR* 4.1 4.0 - - + +
129A SER* 1.3 81.5 + - - +
131A ALA* 1.3 59.4 + - - +
133A ALA* 3.8 2.3 + - - +
134A LEU* 3.1 45.2 + - + +
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Residues in contact with ALA 131 (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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91A VAL* 6.4 0.4 - - - -
127A TYR 3.2 14.8 + - - +
128A ALA 2.6 14.1 + - - +
130A MET* 1.3 70.4 - - - +
132A LYS* 1.3 65.7 + - - +
134A LEU* 4.9 1.6 - - - -
135A LEU* 2.9 48.4 + - + +
144A ILE* 4.8 13.7 - - + -
175A VAL* 3.8 22.7 - - + -
109B PHE* 4.1 4.3 - - + -
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Residues in contact with LYS 132 (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 ALA 2.7 14.0 + - - +
129A SER* 3.4 16.2 - - - +
131A ALA* 1.3 72.9 - - - +
133A ALA* 1.3 57.7 - - + +
135A LEU* 4.5 0.3 - - - +
136A PRO* 3.1 25.8 - - - +
109B PHE* 3.1 56.4 + - + +
110B ASP* 3.5 22.3 + - - +
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Residues in contact with ALA 133 (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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71A LEU* 3.8 29.2 - - + +
74A LEU* 4.4 15.0 - - + -
75A ALA* 3.6 24.1 - - - +
129A SER 3.3 13.2 + - - +
130A MET* 4.1 4.0 - - - +
131A ALA 3.3 0.4 - - - -
132A LYS* 1.3 80.6 - - + +
134A LEU* 1.3 62.5 + - - +
135A LEU 3.5 0.6 + - - -
136A PRO* 3.8 7.6 - - - +
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Residues in contact with LEU 134 (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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11A LEU* 3.7 23.8 - - + -
74A LEU* 3.8 37.7 - - + -
75A ALA* 4.9 0.9 - - - -
78A VAL* 4.8 0.2 - - + -
88A LEU* 4.5 4.3 - - + -
91A VAL* 3.5 41.5 - - + -
130A MET* 3.1 31.7 + - + +
131A ALA* 4.6 1.8 - - - +
133A ALA* 1.3 77.5 - - - +
135A LEU* 1.3 65.6 + - - +
136A PRO 3.5 0.9 - - - -
137A ILE* 3.4 33.3 + - + +
138A MET* 3.3 21.5 + - + +
144A ILE* 6.3 0.4 - - + -
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Residues in contact with LEU 135 (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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131A ALA* 2.9 42.6 + - + +
132A LYS* 4.5 1.1 - - - +
134A LEU* 1.3 77.5 - - - +
136A PRO* 1.3 73.5 - - + +
138A MET* 3.0 35.7 + - - +
144A ILE* 4.0 4.3 - - + -
175A VAL* 5.4 0.2 - - + -
179A ALA* 4.0 18.2 - - + -
182A TYR* 3.7 45.0 - - + +
184A VAL* 4.0 29.2 - - + -
109B PHE* 4.1 16.4 - - + -
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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