Contacts of the helix formed by residues 125 - 146 (chain D) in PDB entry 3P05
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 PRO 125 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D MET* 4.5 9.0 - - + +
123D PRO* 3.7 15.0 - - + +
124D ILE* 1.3 80.5 - - + +
126D VAL* 1.3 64.4 + - - +
127D GLY 3.2 2.7 - - - -
128D GLU* 3.0 23.4 + - + +
129D ILE* 2.9 43.4 + - + +
132D ARG* 5.2 4.9 - - - +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PRO* 3.9 23.6 - - + -
99D PRO* 4.3 13.7 - - + -
103D ASP 5.3 0.2 - - - +
104D ILE* 3.8 30.8 - - + +
114D GLN* 4.0 10.5 - - + +
117D TRP* 4.3 24.5 - - + -
118D MET* 3.6 19.7 - - + +
124D ILE* 2.9 17.3 + - + +
125D PRO* 1.3 71.6 - - - +
127D GLY* 1.3 56.4 + - - +
129D ILE* 3.3 7.0 + - + +
130D TYR* 2.8 37.1 + - - +
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA 3.4 26.2 - - - -
49D PRO* 3.9 10.4 - - - +
52D LEU* 3.6 8.6 - - - +
118D MET* 4.1 7.7 - - - -
125D PRO 3.2 0.8 - - - -
126D VAL* 1.3 84.6 - - - +
128D GLU* 1.3 57.5 + - - +
131D LYS* 2.8 31.6 + - - +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 5.3 2.4 - - - +
46D GLY* 4.6 13.0 + - - -
47D ALA 5.3 2.1 + - - +
125D PRO* 3.0 25.2 + - + +
127D GLY* 1.3 74.9 - - - +
129D ILE* 1.3 58.6 + - - +
131D LYS* 3.3 33.2 + - - +
132D ARG* 3.0 49.6 + - - +
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Residues in contact with ILE 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TRP* 4.1 29.8 - - + -
104D ILE* 3.9 15.5 - - + -
124D ILE* 4.9 5.4 - - + -
125D PRO* 2.9 45.6 + - + +
126D VAL* 3.7 7.2 - - + +
128D GLU* 1.3 73.7 - - - +
130D TYR* 1.3 64.6 + - - +
132D ARG* 3.3 26.9 + - - +
133D TRP* 3.2 51.9 + - + +
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Residues in contact with TYR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D PRO* 3.8 15.0 - - + -
52D LEU* 3.8 20.6 - - + -
53D ASN* 2.8 25.3 + - - -
56D LEU* 4.1 4.0 - - - +
73D ILE* 3.8 26.7 - - + +
104D ILE* 3.3 24.5 - - - +
105D ALA* 3.4 40.4 + - + +
107D THR* 5.8 0.2 - - - +
126D VAL 2.8 20.7 + - - +
127D GLY 3.7 3.6 - - - +
129D ILE* 1.3 71.9 - - - +
131D LYS* 1.3 64.1 + - - +
133D TRP* 3.0 15.2 + + + -
134D ILE* 2.9 43.0 + - + +
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Residues in contact with LYS 131 (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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40D PHE* 3.9 19.5 - - + -
41D SER* 3.5 24.2 + - - +
44D SER* 2.9 48.2 + - - +
45D GLU* 3.7 15.8 + - - +
47D ALA* 5.5 1.3 - - + +
52D LEU* 4.2 11.1 - - + +
127D GLY 2.8 18.5 + - - +
128D GLU* 3.3 34.9 + - - +
129D ILE 3.2 0.4 - - - -
130D TYR* 1.3 75.8 - - - +
132D ARG* 1.3 56.9 + - + +
134D ILE* 3.1 7.4 + - - +
135D ILE* 2.7 41.6 + - + +
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 5.2 5.5 - - - +
128D GLU* 3.0 35.8 + - - +
129D ILE* 3.3 34.7 + - - +
131D LYS* 1.3 72.2 - - + +
133D TRP* 1.3 71.3 + - + +
135D ILE* 3.9 10.9 - - + +
136D LEU* 3.0 24.3 + - - +
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Residues in contact with TRP 133 (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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72D THR* 4.1 7.4 - - - +
73D ILE* 4.4 20.2 - - + +
76D GLU* 3.6 50.9 + - + +
77D ALA* 3.7 24.7 - - + -
80D TRP* 3.8 18.3 - + + -
101D GLY* 3.6 14.6 - - - -
104D ILE* 3.6 32.5 - - + -
105D ALA* 4.5 4.3 - - + -
129D ILE* 3.5 31.6 + - + +
130D TYR* 3.0 22.7 + + - +
132D ARG* 1.3 81.3 - - + +
134D ILE* 1.3 63.1 + - - +
136D LEU* 3.2 8.1 + - + +
137D GLY* 3.1 17.2 + - - -
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Residues in contact with ILE 134 (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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40D PHE* 3.7 25.1 - - + -
52D LEU* 4.0 26.5 - - + -
56D LEU* 3.9 24.5 - - + -
69D LEU* 3.7 10.8 - - + +
73D ILE* 4.0 11.2 - - + -
130D TYR* 2.9 52.2 + - + +
131D LYS* 3.6 5.2 - - - +
133D TRP* 1.3 75.9 - - - +
135D ILE* 1.3 59.5 + - - +
137D GLY* 3.0 4.5 + - - -
138D LEU* 2.8 39.7 + - + +
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 4.1 22.4 - - + -
40D PHE* 4.0 20.9 - - + -
41D SER* 3.6 23.6 - - - +
131D LYS* 2.7 33.8 + - + +
132D ARG* 4.0 9.6 - - + +
134D ILE* 1.3 71.4 - - - +
136D LEU* 1.3 57.3 + - - +
138D LEU* 3.2 7.9 + - + +
139D ASN* 2.8 49.5 + - - +
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Residues in contact with LEU 136 (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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72D THR* 4.0 9.4 - - + -
76D GLU* 3.3 44.0 - - + +
132D ARG 3.0 14.5 + - - +
133D TRP* 3.3 8.7 - - + +
134D ILE 3.1 0.2 - - - -
135D ILE* 1.3 79.9 - - - +
137D GLY* 1.3 61.8 + - - +
139D ASN* 3.2 18.0 + - + +
140D LYS* 3.2 24.8 + - + +
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Residues in contact with GLY 137 (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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69D LEU* 3.6 20.6 - - - -
72D THR* 3.7 22.7 - - - +
133D TRP 3.1 4.4 + - - -
134D ILE 3.0 7.5 + - - -
136D LEU* 1.3 76.0 - - - +
138D LEU* 1.3 62.9 + - - +
140D LYS* 3.3 6.6 + - - +
141D ILE* 3.1 27.5 + - - +
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Residues in contact with LEU 138 (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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23D TRP* 5.4 5.6 - - + -
32D PHE* 4.0 30.5 - - + -
36D VAL* 5.1 7.9 - - + -
37D ILE* 4.0 23.1 - - + -
40D PHE* 4.1 36.6 - - + -
56D LEU* 6.1 1.3 - - + -
69D LEU* 4.1 17.4 - - + +
134D ILE* 2.8 32.1 + - + +
135D ILE* 3.6 10.8 - - + +
137D GLY* 1.3 72.2 - - - +
139D ASN* 1.3 58.5 + - - +
141D ILE* 3.2 5.9 + - + +
142D VAL* 2.9 33.4 + - + +
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Residues in contact with ASN 139 (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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37D ILE* 3.0 19.2 - - - +
135D ILE* 2.8 42.2 + - - +
136D LEU* 3.2 13.2 + - + +
138D LEU* 1.3 71.8 - - - +
140D LYS* 1.3 63.3 + - + +
142D VAL* 3.5 1.8 + - - +
143D ARG* 3.0 34.2 + - - +
176D GLN* 2.9 41.7 + - - +
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Residues in contact with LYS 140 (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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212C GLU* 3.1 40.2 + - - +
68D MET* 6.0 4.0 - - - -
72D THR* 2.9 36.8 + - + +
75D GLU* 3.9 17.8 + - - -
136D LEU* 3.2 27.7 + - + +
137D GLY 3.6 6.3 - - - +
138D LEU 3.3 0.2 - - - -
139D ASN* 1.3 76.8 - - + +
141D ILE* 1.3 58.5 + - + +
143D ARG* 3.3 18.9 + - - +
144D MET* 3.0 33.0 + - + +
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Residues in contact with ILE 141 (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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32D PHE* 3.7 33.2 - - + -
65D ALA* 3.3 39.3 - - + +
68D MET* 4.7 17.0 - - + -
69D LEU* 4.0 19.5 - - + +
137D GLY 3.1 18.4 + - - +
138D LEU* 3.7 13.7 - - + +
140D LYS* 1.3 75.2 - - + +
142D VAL* 1.3 60.7 + - - +
144D MET* 3.2 5.9 + - - +
145D TYR* 2.9 42.6 + - + +
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Residues in contact with VAL 142 (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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32D PHE* 3.4 34.1 - - + +
33D SER 4.1 9.0 - - - +
34D PRO* 3.9 21.1 - - + -
36D VAL* 5.5 1.3 - - + -
37D ILE* 4.1 19.1 - - + -
138D LEU* 2.9 20.9 + - + +
139D ASN* 3.8 5.8 - - - +
141D ILE* 1.3 76.6 - - - +
143D ARG* 1.3 62.6 + - - +
145D TYR* 3.5 1.4 + - - +
146D SER* 3.1 23.6 + - - -
174D ALA* 4.1 25.8 - - + +
176D GLN* 4.3 6.5 - - - +
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Residues in contact with ARG 143 (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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139D ASN* 3.0 35.8 + - - +
140D LYS* 3.7 14.7 - - - +
141D ILE 3.2 0.2 - - - -
142D VAL* 1.3 77.2 - - - +
144D MET* 1.3 60.9 + - + +
146D SER 3.0 26.5 - - - +
147D PRO* 3.4 7.1 - - + +
174D ALA 4.0 20.0 + - - +
175D GLU* 4.0 22.7 + - + +
176D GLN* 3.8 20.8 + - - -
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Residues in contact with MET 144 (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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162C ARG* 4.1 10.6 + - - +
212C GLU* 4.2 17.9 - - + +
215C MET* 3.7 39.5 - - + +
216C THR* 3.9 17.3 - - - +
219C GLN* 3.9 26.2 - - - +
68D MET* 3.9 26.5 - - + +
140D LYS 3.0 20.8 + - - +
141D ILE* 3.2 6.7 + - - +
143D ARG* 1.3 73.0 - - + +
145D TYR* 1.3 67.4 + - + +
146D SER 3.0 5.6 + - - -
147D PRO* 3.5 22.1 - - - +
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Residues in contact with TYR 145 (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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162C ARG* 3.5 55.9 + - + +
166C ASP* 4.4 4.3 + - - -
215C MET* 5.7 0.9 - - + -
31D ALA* 4.3 12.1 - - + -
32D PHE* 3.8 40.8 - + + +
62D HIS* 2.8 37.1 + + - +
65D ALA* 4.2 10.5 - - + +
68D MET* 5.6 5.6 - - + -
141D ILE* 2.9 31.0 + - + +
142D VAL 4.1 2.9 - - - +
144D MET* 1.3 81.2 - - + +
146D SER* 1.3 59.3 + - - +
147D PRO* 3.7 5.9 - - - +
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Residues in contact with SER 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE 6.0 0.7 - - - -
34D PRO* 6.1 1.1 - - - -
142D VAL* 3.1 15.2 + - - -
143D ARG* 3.0 13.7 - - - +
144D MET 3.0 0.4 - - - -
145D TYR* 1.3 79.6 - - - +
147D PRO* 1.3 64.4 - - - +
148D THR* 3.5 7.3 + - - +
170D LYS* 5.4 12.6 - - - +
171D THR* 4.6 13.0 + - - +
174D ALA* 3.5 25.3 - - - +
175D GLU* 5.6 3.6 - - - +
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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
------------------------------------------------------------
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