Contacts of the helix formed by residues 119 - 135 (chain D) in PDB entry 3G1Q
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 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D ARG* 3.6 7.0 - - - +
113D GLY 5.5 0.2 - - - +
117D ALA 4.5 1.3 - - - +
118D ALA* 1.4 84.9 - - + +
120D TYR* 1.3 62.5 + - - +
121D PRO* 3.3 9.6 - - + -
122D ARG* 3.0 16.7 + - + -
123D MET 2.8 24.1 + - - -
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Residues in contact with TYR 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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94D ASN* 3.7 35.1 + - + +
95D GLU* 3.7 46.7 - - + +
98D SER* 2.6 32.6 + - - -
99D PRO* 4.1 7.6 - - + -
100D ARG* 3.2 39.6 + - + +
101D GLU* 5.0 0.3 + - - -
116D TYR 5.4 0.2 - - - -
119D PRO* 1.3 70.6 - - - +
121D PRO* 1.4 66.3 - - + +
123D MET* 3.6 18.0 - - + +
124D ARG* 2.9 28.2 + - - +
364D MET* 4.6 7.4 - - - +
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Residues in contact with PRO 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLU* 5.5 3.6 - - - +
119D PRO* 3.4 11.7 - - + -
120D TYR* 1.4 93.9 - - + +
122D ARG* 1.3 56.1 + - - +
124D ARG* 3.5 6.0 + - + +
125D GLU* 3.0 34.5 + - - +
271D ARG* 3.6 21.7 + - - +
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Residues in contact with ARG 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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113D GLY 5.3 0.4 - - - +
118D ALA* 3.5 18.8 - - + -
119D PRO* 3.0 19.8 + - + +
121D PRO* 1.3 79.1 - - - +
123D MET* 1.3 65.1 + - - +
125D GLU* 3.2 12.1 + - - +
126D GLN* 3.0 39.4 + - - +
270D TYR* 3.7 47.0 - - - +
272D ASP* 4.3 16.6 + - - +
274D THR* 4.5 5.7 + - - -
280D GLU* 4.0 14.5 + - - -
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Residues in contact with MET 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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94D ASN* 3.3 33.0 - - - +
99D PRO* 4.0 8.7 - - - -
115D ALA* 3.2 31.4 - - - +
116D TYR* 3.8 30.5 - - - +
118D ALA* 3.7 4.9 - - - +
119D PRO 2.8 16.1 + - - +
120D TYR* 3.6 23.8 - - + +
122D ARG* 1.3 74.1 - - - +
124D ARG* 1.3 80.3 + - - +
126D GLN* 3.1 8.1 + - - +
127D LEU* 2.9 34.4 + - + +
420D HIS* 3.7 8.7 - - + -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ASN* 3.7 12.3 - - - +
120D TYR 2.9 18.6 + - - +
121D PRO* 3.8 7.2 - - + +
122D ARG 3.2 0.4 - - - -
123D MET* 1.3 101.3 - - - +
125D GLU* 1.3 59.0 + - + +
127D LEU* 3.4 17.3 + - - +
128D ASN* 2.9 51.9 + - - +
271D ARG* 6.0 0.2 - - - +
419D VAL* 3.4 22.4 + - - +
420D HIS* 4.0 4.9 + - - -
423D ILE* 6.1 1.6 - - - +
480D HEM 3.3 24.9 + - - -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PRO 3.0 18.6 + - - +
122D ARG* 3.6 15.4 + - - +
123D MET 3.2 0.2 - - - -
124D ARG* 1.3 77.9 - - + +
126D GLN* 1.3 62.2 + - - +
128D ASN* 3.3 11.1 + - - +
129D PHE* 3.0 35.7 + - + -
269D VAL 4.7 0.2 - - - +
270D TYR* 3.2 30.6 - - + +
271D ARG* 2.8 64.0 + - - +
272D ASP* 4.9 1.7 + - - +
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Residues in contact with GLN 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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113D GLY 4.4 6.5 + - - -
114D VAL* 3.8 4.1 - - - +
115D ALA* 2.7 35.6 + - - +
118D ALA* 4.3 0.5 - - - +
122D ARG* 3.0 36.9 + - - +
123D MET* 3.6 5.3 - - - +
125D GLU* 1.3 77.3 - - - +
127D LEU* 1.3 62.9 + - - +
129D PHE* 3.1 12.1 + - - +
130D LEU 3.1 17.5 + - - -
270D TYR* 3.1 30.6 + - + +
276D MET* 4.8 8.1 - - - -
280D GLU* 3.8 19.8 + - - +
284D MET* 3.7 28.1 - - + +
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Residues in contact with LEU 127 (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 ALA* 5.2 4.9 - - + -
116D TYR* 4.1 14.6 - - + +
123D MET* 2.9 42.5 + - + +
124D ARG* 3.5 33.9 - - - +
126D GLN* 1.3 76.4 - - + +
128D ASN* 1.3 59.2 + - - +
130D LEU* 3.5 0.6 + - - -
131D ALA* 2.9 30.0 + - - +
284D MET* 4.2 18.6 - - + -
287D ALA* 6.3 1.1 - - + -
420D HIS* 4.3 1.6 - - - +
423D ILE* 3.5 10.5 - - + +
480D HEM 3.5 43.5 - - + +
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Residues in contact with ASN 128 (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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124D ARG* 2.9 49.6 + - - +
125D GLU* 3.4 10.5 - - - +
127D LEU* 1.3 77.5 - - - +
129D PHE* 1.3 57.0 + - + +
131D ALA* 3.3 7.5 + - - +
132D GLU* 2.9 43.1 + - - +
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Residues in contact with PHE 129 (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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125D GLU* 3.0 27.4 + - + -
126D GLN* 3.1 12.1 + - - +
128D ASN* 1.3 74.4 - - + +
130D LEU* 1.3 66.3 + - - +
132D GLU* 3.5 23.7 + - - +
133D GLU* 3.3 25.1 + - - +
265D LEU* 4.1 15.2 - - + +
268D ALA* 3.7 22.9 - - + -
269D VAL 3.4 30.1 - - - -
270D TYR* 3.7 33.7 - + - -
276D MET* 3.7 21.3 - - + -
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Residues in contact with LEU 130 (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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126D GLN 3.1 9.5 + - - +
127D LEU 3.7 7.4 - - - +
129D PHE* 1.3 78.2 - - - +
131D ALA* 1.3 66.1 + - - +
133D GLU* 2.9 13.4 + - - +
134D LEU* 3.1 30.9 + - + +
261D LEU* 4.1 23.6 - - + -
265D LEU* 4.1 13.6 - - + +
284D MET* 4.0 38.1 - - + +
287D ALA* 4.8 1.3 - - + -
288D ALA* 4.2 21.3 - - + +
423D ILE* 3.8 5.8 - - + -
480D HEM 3.6 30.1 - - + -
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Residues in contact with ALA 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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127D LEU 2.9 18.6 + - - +
128D ASN* 3.6 10.8 - - - +
130D LEU* 1.3 75.3 - - - +
132D GLU* 1.3 62.0 + - - +
134D LEU* 3.0 5.7 + - - +
135D THR* 3.0 30.2 + - + +
423D ILE* 3.4 36.7 - - + +
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Residues in contact with GLU 132 (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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128D ASN* 2.9 31.0 + - + +
129D PHE* 3.7 23.6 - - - +
130D LEU 3.2 0.2 - - - -
131D ALA* 1.3 75.7 - - + +
133D GLU* 1.3 64.7 + - - +
134D LEU 3.3 0.2 - - - -
135D THR* 3.3 24.1 + - + -
138D LYS* 3.5 12.6 - - - -
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Residues in contact with GLU 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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129D PHE 3.3 14.5 + - - +
130D LEU 2.9 9.3 + - - +
132D GLU* 1.3 81.2 - - - +
134D LEU* 1.3 63.5 + - + +
135D THR 3.4 0.9 - - - -
138D LYS* 3.7 36.2 + - - +
142D PHE* 4.5 7.4 - - - -
183D LEU* 5.1 2.1 - - - +
260D ASP 3.8 10.6 - - - +
261D LEU* 3.5 32.3 - - + -
264D GLY* 3.4 35.2 - - - +
265D LEU* 4.3 11.2 - - + -
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Residues in contact with LEU 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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130D LEU* 3.4 39.3 - - + +
131D ALA 3.0 5.0 + - - +
133D GLU* 1.3 81.0 - - + +
135D THR* 1.3 65.3 + - - +
139D PHE* 3.3 20.1 - - - -
142D PHE* 5.4 1.6 - - - -
183D LEU* 4.0 28.9 - - + -
261D LEU* 5.3 1.3 - - + -
288D ALA* 5.4 0.7 - - + -
423D ILE* 3.8 33.1 - - + +
424D GLY* 4.2 4.0 - - - -
426D LYS* 5.5 1.2 - - - +
427D PHE* 4.3 13.2 + - + +
480D HEM 3.6 41.1 - - + -
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Residues in contact with THR 135 (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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131D ALA* 3.0 25.4 + - + +
132D GLU* 3.3 22.7 + - + -
133D GLU 3.4 0.6 - - - -
134D LEU* 1.3 80.2 - - - +
136D ILE* 1.3 89.6 + - + +
137D ALA* 3.3 6.9 + - - +
138D LYS* 3.4 15.4 + - - +
139D PHE* 3.2 13.9 - - - -
423D ILE 5.8 0.4 - - - -
426D LYS* 6.2 0.9 - - - -
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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