Contacts of the helix formed by residues 119 - 138 (chain D) in PDB entry 4GTU
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 PHE 119 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 4.4 18.8 - - + -
114D CYS* 4.4 7.0 - - - -
116D SER 3.1 6.6 + - - +
117D PRO 3.1 4.0 + - - +
118D ASP* 1.3 74.4 - - - +
120D GLU* 1.3 91.6 + - - +
121D LYS 2.9 1.9 + - - -
122D LEU* 3.1 2.4 + - - -
123D LYS* 2.8 50.5 + - + +
169D PHE* 3.9 26.5 - + - -
213D VAL* 3.6 44.9 - - + -
214D TRP* 3.5 39.9 - + + -
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP 3.2 1.0 + - - -
119D PHE* 1.3 107.8 - - - +
121D LYS* 1.3 59.3 + - + +
123D LYS* 4.8 4.2 - - + +
124D PRO* 3.3 21.7 - - - +
213D VAL* 5.7 2.1 - - - +
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ASP* 2.8 47.2 + - + +
120D GLU* 1.3 76.0 - - + +
122D LEU* 1.3 70.8 + - + +
123D LYS 3.4 0.2 - - - -
124D PRO* 3.6 10.6 - - - +
125D GLU* 3.8 11.5 + - - +
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Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D VAL* 3.7 24.2 - - + +
116D SER* 4.0 28.9 - - - +
118D ASP* 3.1 30.6 + - + +
119D PHE* 4.1 2.7 - - - +
121D LYS* 1.3 81.7 - - + +
123D LYS* 1.3 59.1 + - - +
125D GLU* 3.3 26.2 - - - +
126D TYR* 2.9 30.5 + - - +
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Residues in contact with LYS 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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113D VAL* 4.7 7.3 - - - +
119D PHE* 2.8 36.7 + - + +
120D GLU* 4.8 2.7 - - - +
122D LEU* 1.3 74.2 - - - +
124D PRO* 1.3 69.9 - - + +
126D TYR* 2.9 8.2 + - - +
127D LEU* 2.8 46.5 + - + +
169D PHE* 3.4 55.4 + - + -
170D GLU* 5.0 3.1 - - - -
214D TRP* 5.9 0.4 - - - -
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Residues in contact with PRO 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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120D GLU 3.3 21.3 - - - +
121D LYS 3.6 7.4 - - - +
123D LYS* 1.3 98.1 - - + +
125D GLU* 1.3 61.0 + - - +
127D LEU* 3.2 15.9 + - + +
128D GLU* 3.1 28.1 + - - +
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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
----------------------------------------------------------
113D VAL* 5.9 0.3 - - - +
121D LYS 3.8 9.2 + - - +
122D LEU* 3.3 33.5 - - - +
123D LYS 3.0 0.2 - - - -
124D PRO* 1.3 80.4 - - - +
126D TYR* 1.3 62.0 + - - +
128D GLU* 3.1 30.7 - - - +
129D GLU* 3.1 18.2 - - - +
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Residues in contact with TYR 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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106D VAL* 3.7 10.0 + - - +
109D GLN* 4.0 35.4 - - + +
110D LEU* 3.9 19.7 - - + -
113D VAL* 4.3 14.1 - - + -
122D LEU 2.9 15.6 + - - +
123D LYS* 2.9 6.0 + - - +
125D GLU* 1.3 72.3 + - - +
127D LEU* 1.3 69.3 + - - +
128D GLU 3.0 3.8 + - - -
129D GLU* 3.0 20.8 + - - +
130D LEU* 3.2 15.9 + - + -
133D MET* 3.3 34.6 - - + -
166D HIS* 2.7 41.4 + + - -
169D PHE* 5.0 9.6 - + - -
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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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123D LYS* 2.8 33.6 + - + +
124D PRO* 3.2 20.6 + - + +
126D TYR* 1.3 74.9 - - - +
128D GLU* 1.3 60.6 + - - +
130D LEU* 3.3 16.3 + - + -
131D PRO* 3.1 23.7 - - + +
169D PHE* 6.3 1.8 - - + -
170D GLU* 3.3 39.0 - - + +
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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
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124D PRO* 3.1 19.6 + - + +
125D GLU* 3.1 29.1 - - - +
126D TYR 3.0 0.6 + - - -
127D LEU* 1.3 77.4 - - - +
129D GLU* 1.3 68.5 + - - +
131D PRO* 3.4 14.4 - - - +
132D THR* 5.3 0.9 + - - -
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Residues in contact with GLU 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* 3.1 25.4 - - - +
126D TYR* 3.0 12.5 + - - +
128D GLU* 1.3 90.3 - - + +
130D LEU* 1.3 65.8 + - - +
131D PRO* 3.3 3.4 - - - -
132D THR* 3.3 14.1 + - + +
133D MET* 3.2 36.8 + - + +
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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 TYR* 3.2 17.8 + - + +
127D LEU* 3.5 24.5 - - + +
129D GLU* 1.3 77.9 - - - +
131D PRO* 1.3 65.7 - - + +
133D MET* 3.2 23.7 - - - +
134D MET* 3.1 37.1 + - - +
166D HIS* 3.3 32.1 - - + -
169D PHE* 5.9 2.9 - - + -
170D GLU* 3.9 18.2 - - + -
173D CYS* 3.3 30.3 - - + -
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Residues in contact with PRO 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* 3.1 20.2 - - + +
128D GLU 3.4 12.8 - - - +
129D GLU 3.4 0.7 - - - -
130D LEU* 1.3 91.1 - - + +
132D THR* 1.3 57.4 + - - +
134D MET* 3.4 5.6 + - + +
135D GLN* 3.0 24.0 + - - +
177D PHE* 3.5 15.2 - - + -
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Residues in contact with THR 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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49C LYS* 5.4 6.1 - - - +
50C PHE* 5.9 2.7 - - + -
128D GLU 5.3 0.6 + - - -
129D GLU* 3.3 14.5 + - + +
130D LEU 3.3 0.2 - - - -
131D PRO* 1.3 78.5 - - - +
133D MET* 1.3 68.4 + - + +
135D GLN* 3.2 16.1 + - - +
136D HIS* 3.1 46.1 + - + +
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Residues in contact with MET 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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56C PHE* 4.8 1.9 - - - -
106D VAL* 4.4 17.0 - - + -
109D GLN* 4.4 9.9 - - - +
126D TYR* 3.3 42.8 - - + -
129D GLU* 3.2 36.1 + - + +
130D LEU* 3.2 30.7 - - + +
132D THR* 1.3 80.1 - - + +
134D MET* 1.3 63.9 + - - +
136D HIS* 3.3 14.0 + - - +
137D PHE* 3.3 26.9 + - + -
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Residues in contact with MET 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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106D VAL* 6.1 1.1 - - - -
130D LEU* 3.1 38.7 + - - +
131D PRO* 3.5 1.6 - - + +
133D MET* 1.3 78.6 - - - +
135D GLN* 1.3 65.0 + - - +
137D PHE* 3.0 34.4 + - + +
138D SER* 3.3 5.0 + - - -
162D VAL* 5.2 1.3 - - + +
163D LEU* 3.6 33.4 - - + -
166D HIS* 4.4 18.8 - - + +
173D CYS* 3.6 25.8 - - + +
174D LEU* 3.9 13.2 - - + -
177D PHE* 3.5 22.4 - - + -
180D LEU* 3.8 11.7 - - + +
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Residues in contact with GLN 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 PRO 3.0 11.8 + - - +
132D THR* 3.4 19.5 + - - +
134D MET* 1.3 77.2 - - - +
136D HIS* 1.3 65.3 + - - +
138D SER* 2.9 8.3 + - - -
139D GLN* 2.8 53.7 + - + +
177D PHE* 3.6 29.4 - - + -
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Residues in contact with HIS 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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49C LYS* 4.8 7.9 - - - -
50C PHE* 5.3 6.6 - + - -
54C LEU 5.4 0.2 - - - -
55C ASP 4.0 11.3 - - - +
56C PHE* 3.6 27.1 - - + -
57C PRO* 3.7 36.8 - - + +
132D THR* 3.1 41.6 + - + +
133D MET* 3.5 12.1 - - - +
134D MET 3.2 0.2 - - - -
135D GLN* 1.3 82.7 + - - +
137D PHE* 1.3 62.4 + - - +
139D GLN* 3.2 34.5 + - - +
140D PHE* 3.3 9.7 + - - +
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Residues in contact with PHE 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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56C PHE* 3.6 19.9 - + - -
99D LEU* 3.6 26.7 - - + -
102D GLN* 5.4 2.2 - - + -
103D ALA* 4.7 11.2 - - + -
106D VAL* 4.1 29.8 - - + -
133D MET* 3.3 16.4 + - + -
134D MET* 3.0 31.6 + - + +
136D HIS* 1.3 74.8 - - - +
138D SER* 1.3 66.4 + - - +
140D PHE* 3.0 12.8 + - - +
141D LEU* 3.0 11.4 + - - +
147D PHE* 3.5 23.9 - + + -
159D ALA* 5.5 6.1 - - + -
162D VAL* 4.2 20.2 - - + -
163D LEU* 4.4 8.7 - - + -
180D LEU* 4.0 15.0 - - + -
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Residues in contact with SER 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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134D MET 3.3 2.7 + - - -
135D GLN* 2.9 12.6 + - - -
137D PHE* 1.3 73.2 - - - +
139D GLN* 1.3 58.4 + - - +
140D PHE 2.9 7.1 + - - -
142D GLY* 2.8 32.6 + - - -
177D PHE* 3.3 32.3 - - - +
179D ASN* 2.8 28.1 + - - +
180D LEU* 3.4 7.3 - - - +
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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