Contacts of the helix formed by residues 111 - 126 (chain D) in PDB entry 1P4A
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 LYS 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C PRO* 4.6 14.6 - - + -
107D ASP* 3.5 35.0 + - - +
108D ILE* 3.5 16.2 + - - +
109D LEU 3.8 0.6 - - - -
110D GLY* 1.3 75.0 - - - +
112D PRO* 1.3 65.3 - - + +
113D SER* 3.2 11.7 - - - +
114D VAL* 2.9 23.5 + - + +
115D LEU* 2.8 29.1 + - - +
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Residues in contact with PRO 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TYR* 4.4 12.2 + - + +
149C ALA* 3.8 20.0 - - + +
150C SER* 4.1 18.6 - - - +
153C ASN* 4.4 13.2 - - - +
154C VAL 3.1 32.1 - - - +
156C VAL 4.6 0.7 - - - +
110D GLY 3.2 12.6 - - - +
111D LYS* 1.3 83.9 - - + +
113D SER* 1.3 57.1 + - - +
115D LEU* 4.2 8.3 - - + -
116D SER* 2.8 35.9 + - - -
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Residues in contact with SER 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN* 4.6 11.9 + - - -
83D PHE* 5.1 0.7 - - - -
111D LYS* 3.2 16.7 + - - +
112D PRO* 1.3 77.9 - - - +
114D VAL* 1.3 66.5 + - - +
116D SER* 4.2 4.4 - - - -
117D LYS* 3.7 22.7 + - - +
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D PHE* 3.9 10.7 - - + -
87D LEU* 4.3 18.2 - - + -
108D ILE* 3.9 36.3 - - + +
111D LYS* 2.9 30.0 + - + +
113D SER* 1.3 81.3 + - - +
115D LEU* 1.3 66.0 + - + +
117D LYS* 3.3 4.7 + - - +
118D VAL* 3.1 34.4 + - + +
232D LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.4 37.0 - - + +
108D ILE 4.2 6.5 - - - +
109D LEU* 3.6 33.2 - - + +
110D GLY* 4.0 2.9 - - - -
111D LYS 2.8 31.3 + - - +
112D PRO 4.0 1.6 - - - +
114D VAL* 1.3 70.5 - - + +
116D SER* 1.3 59.8 + - - +
118D VAL* 4.0 4.4 - - + +
119D GLY 2.8 26.7 + - - -
143D PRO* 3.8 10.1 - - + -
144D LEU* 3.9 35.8 - - + +
147D ALA* 3.4 12.8 - - + +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TYR* 4.2 7.9 + - - -
112D PRO 2.8 23.0 + - - -
113D SER* 4.2 6.1 - - - -
115D LEU* 1.3 72.4 - - - +
117D LYS* 1.3 60.6 + - - +
120D LYS* 2.9 25.3 + - - +
147D ALA* 4.8 0.7 - - - -
151D TYR* 3.1 33.9 + - - -
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C HIS* 6.0 4.3 + - - -
75D MET* 3.4 15.8 - - + +
79D GLU* 3.3 26.9 + - - +
83D PHE* 3.6 42.8 - - + -
113D SER 3.7 13.2 + - - +
114D VAL 3.3 4.0 + - - +
115D LEU 3.3 0.6 - - - -
116D SER* 1.3 79.1 - - - +
118D VAL* 1.3 59.2 + - - +
120D LYS* 4.3 8.5 - - - +
121D LEU* 2.9 24.6 + - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 3.6 23.8 - - + -
87D LEU* 4.1 3.6 - - + -
114D VAL* 3.1 24.1 + - + +
115D LEU* 4.0 4.7 - - + +
117D LYS* 1.3 72.7 - - - +
119D GLY* 1.3 65.5 + - - +
121D LEU* 3.1 8.1 + - - +
122D PHE* 3.0 35.1 + - + -
144D LEU* 3.6 26.2 - - + -
232D LEU* 4.1 24.2 - - + -
249D LEU* 4.1 13.9 - - + -
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Residues in contact with GLY 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU 2.8 21.4 + - - -
116D SER 3.9 0.9 - - - -
118D VAL* 1.3 73.9 - - - +
120D LYS* 1.3 56.7 + - - +
122D PHE* 3.4 5.6 + - - +
123D ALA* 2.9 29.6 + - - +
144D LEU* 4.6 2.2 - - - +
147D ALA* 4.1 3.6 - - - -
148D ALA* 3.6 28.9 - - - -
151D TYR* 3.8 6.7 - - - -
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Residues in contact with LYS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLY 3.1 13.9 + - - -
56D ILE* 3.0 27.4 + - - +
71D TYR* 4.8 2.2 - - - -
73D PRO* 4.5 9.4 - - + -
74D LYS 3.1 28.6 + - - +
75D MET* 4.1 18.5 - - + +
79D GLU* 4.7 5.6 + - - +
116D SER 2.9 18.9 + - - +
117D LYS* 3.7 10.8 - - - +
119D GLY* 1.3 75.9 - - - +
121D LEU* 1.3 58.1 + - - +
123D ALA* 3.7 1.1 - - - +
124D SER* 2.8 28.6 + - - -
151D TYR* 3.5 35.5 - - + +
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D MET* 3.9 15.7 - - + +
80D ALA* 4.0 16.8 - - + -
83D PHE* 4.6 6.1 - - + -
84D VAL* 3.9 19.3 - - + -
117D LYS 2.9 17.2 + - - +
118D VAL* 3.1 7.6 + - - +
120D LYS* 1.3 77.1 - - - +
122D PHE* 1.3 62.4 + - + +
124D SER* 3.3 2.8 + - - -
125D VAL* 3.0 26.9 + - + +
247D MET* 5.2 0.9 - - + -
249D LEU* 3.8 35.2 - - + -
269D PHE* 4.9 3.1 - - + -
273D PHE* 3.6 35.9 - - + -
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 3.0 26.5 + - + -
119D GLY 3.6 6.3 - - - +
121D LEU* 1.3 76.3 - - - +
123D ALA* 1.3 63.8 + - - +
125D VAL 3.3 1.6 + - - -
126D PHE* 3.0 34.3 + + + +
144D LEU* 3.6 31.9 - - + -
148D ALA* 4.1 13.2 - - + -
152D LEU* 5.0 1.3 - - - -
200D LEU* 5.2 1.1 - - + -
202D ILE* 3.6 28.5 - - + -
230D GLY* 3.8 15.0 - - - -
231D VAL* 3.7 30.3 - - - -
232D LEU* 4.0 3.8 - - - -
247D MET* 3.4 29.6 - - + -
249D LEU* 4.2 15.7 - - + -
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Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D HIS* 4.8 0.8 + - - +
73D PRO* 4.4 6.6 - - + +
119D GLY 2.9 13.6 + - - +
120D LYS 3.8 3.4 - - - +
122D PHE* 1.3 76.2 - - - +
124D SER* 1.3 57.4 + - - +
126D PHE 3.7 0.6 - - - +
127D ALA* 2.9 31.5 + - - +
148D ALA 4.0 1.1 - - - +
151D TYR* 3.4 34.5 - - + +
152D LEU* 3.7 32.1 - - + +
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D PRO 3.8 10.0 + - - -
74D LYS* 2.5 43.5 + - - +
75D MET* 2.9 41.7 + - - -
120D LYS 2.8 18.3 + - - -
121D LEU* 3.6 6.3 - - - -
122D PHE 3.2 0.2 - - - -
123D ALA* 1.3 75.7 - - - +
125D VAL* 1.3 65.0 + - - +
127D ALA* 3.5 5.4 - - - +
128D GLU* 4.1 0.2 - - - +
273D PHE* 4.9 4.3 - - - -
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 3.0 22.7 + - + +
122D PHE 3.7 3.8 - - - +
124D SER* 1.3 77.2 - - - +
126D PHE* 1.3 72.0 + - + +
127D ALA 3.3 0.9 + - - -
128D GLU* 4.0 8.1 - - - +
129D ARG* 5.0 5.1 + - - +
247D MET* 3.6 33.9 - - + -
272D PHE* 3.7 41.9 - - + +
273D PHE* 3.9 27.6 - - + -
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 3.0 28.4 + + + +
123D ALA* 3.7 3.1 - - - +
125D VAL* 1.3 88.7 - - + +
127D ALA* 1.3 64.0 + - - +
128D GLU 3.2 3.1 - - - -
129D ARG* 3.1 61.2 + - + +
131D ILE* 3.7 24.5 - - + +
152D LEU* 4.5 2.6 - - + +
200D LEU* 3.7 27.8 - - + -
227D ALA 4.8 0.2 - - - -
228D GLY* 4.0 11.0 - - - -
229D ILE 3.6 27.4 - - - -
230D GLY* 4.2 5.6 - - - -
245D GLU* 5.0 1.1 - - - -
247D MET* 3.9 26.7 - - + -
272D PHE* 4.7 3.8 - + - -
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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
------------------------------------------------------------
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