Contacts of the helix formed by residues 119 - 141 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113H VAL* 3.4 28.3 - - + -
114H CYS* 3.9 23.8 - - - -
116H SER* 3.2 5.9 + - - +
117H PRO 3.1 6.0 + - - +
118H ASP* 1.3 73.1 - - - +
120H GLU* 1.3 70.6 + - + +
122H LEU* 2.8 9.7 + - - +
123H LYS* 2.5 71.9 + - + -
169H PHE* 3.8 7.9 - + - -
213H VAL* 3.4 24.5 - - + -
214H TRP* 3.7 35.9 - + + -
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ASP 3.3 0.8 - - - -
119H PHE* 1.3 93.4 - - + +
121H LYS* 1.3 60.5 + - - +
123H LYS* 3.8 10.0 - - + +
124H PRO* 3.1 21.0 - - - +
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Residues in contact with LYS 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H ASP* 3.0 41.6 + - + +
120H GLU* 1.3 78.6 - - - +
122H LEU* 1.3 70.7 + - + +
123H LYS 3.5 0.2 - - - -
124H PRO* 4.0 6.2 - - - +
125H GLU* 3.8 11.4 + - - +
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Residues in contact with LEU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 4.1 29.2 - - + -
116H SER* 4.2 20.0 - - - +
118H ASP* 3.5 19.1 - - + +
119H PHE* 2.8 7.6 + - - +
121H LYS* 1.3 94.2 - - + +
123H LYS* 1.3 64.4 + - - +
124H PRO 3.3 2.5 - - - -
125H GLU* 3.0 44.2 - - - +
126H TYR* 3.2 11.0 + - - +
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Residues in contact with LYS 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 5.7 2.5 - - - -
119H PHE* 2.5 49.2 + - + +
120H GLU* 3.8 11.4 - - + +
122H LEU* 1.3 72.9 - - - +
124H PRO* 1.4 68.5 - - + +
126H TYR* 3.9 6.2 - - - +
127H LEU* 3.2 44.0 + - + +
169H PHE* 3.3 44.1 + - + -
214H TRP* 5.1 4.4 - - - +
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Residues in contact with PRO 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H GLU 3.1 19.3 - - - +
121H LYS 4.0 5.2 - - - +
122H LEU 3.6 2.7 - - - -
123H LYS* 1.4 92.0 - - + +
125H GLU* 1.3 54.7 + - - +
126H TYR 3.2 2.0 - - - -
127H LEU* 3.1 9.5 + - + +
128H GLU* 2.7 44.1 + - + +
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LYS* 3.8 12.9 + - - +
122H LEU* 3.0 49.9 - - + +
124H PRO* 1.3 79.0 - - - +
126H TYR* 1.3 61.1 + - + +
128H GLU* 3.4 22.6 + - - +
129H GLU* 2.9 27.0 + - - +
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Residues in contact with TYR 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H VAL 4.0 6.4 + - - -
109H GLN* 3.5 21.3 - - + -
110H LEU* 3.8 29.4 - - + -
113H VAL* 4.8 19.1 - - + -
122H LEU 3.2 11.8 + - - +
123H LYS* 3.9 2.7 - - - +
125H GLU* 1.3 81.5 - - + +
127H LEU* 1.3 61.9 + - - +
128H GLU 3.2 0.5 + - - -
129H GLU* 3.2 14.6 + - + +
130H LEU* 3.0 43.8 + - + +
133H MET* 3.4 31.6 - - + -
166H HIS* 2.7 32.5 + - - -
169H PHE* 4.1 22.4 - + - -
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Residues in contact with LEU 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H LYS* 3.2 41.7 + - + +
124H PRO* 3.1 10.2 + - + +
126H TYR* 1.3 82.9 - - - +
128H GLU* 1.3 59.2 + - - +
130H LEU* 3.5 14.7 - - + +
131H PRO* 3.3 21.2 - - + +
169H PHE* 5.0 5.8 - - + -
170H GLU* 3.6 43.5 - - + +
173H CYS* 6.0 0.2 - - + -
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PRO* 2.7 20.8 + - + +
125H GLU* 3.6 21.2 + - - +
126H TYR 3.1 0.4 - - - -
127H LEU* 1.3 75.3 - - - +
129H GLU* 1.3 59.6 + - + +
131H PRO* 3.6 8.8 - - - +
132H THR* 5.8 1.7 - - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H GLU* 2.9 21.0 - - - +
126H TYR* 3.4 19.8 - - + +
128H GLU* 1.3 76.0 - - + +
130H LEU* 1.3 63.0 + - - +
131H PRO* 3.3 3.4 - - - -
132H THR* 2.9 30.5 + - - +
133H MET* 3.3 21.0 + - + +
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Residues in contact with LEU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H TYR* 3.0 32.1 + - + +
127H LEU* 3.5 16.4 - - + +
129H GLU* 1.3 77.9 - - - +
131H PRO* 1.3 68.6 - - + +
133H MET* 3.2 32.7 - - + +
134H MET* 3.0 26.7 + - - +
166H HIS* 3.4 25.1 - - + -
169H PHE* 5.2 4.5 - - + -
170H GLU* 4.4 15.5 - - + -
173H CYS* 3.9 33.7 - - + -
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Residues in contact with PRO 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H LEU* 3.3 17.0 - - + +
128H GLU 3.6 8.5 - - - +
129H GLU 3.5 3.4 - - - -
130H LEU* 1.3 92.5 - - + +
132H THR* 1.3 58.5 + - + +
134H MET* 3.3 1.1 + - + -
135H GLN* 2.8 31.3 + - - +
173H CYS* 5.7 7.9 - - + -
177H PHE* 3.4 18.4 - - + -
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Residues in contact with THR 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H GLU 5.8 1.1 - - - +
129H GLU* 2.9 27.6 + - - +
131H PRO* 1.3 78.3 - - + +
133H MET* 1.3 60.9 + - - +
135H GLN* 3.2 29.7 - - - +
136H HIS* 3.1 29.8 + - - -
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Residues in contact with MET 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G PHE* 5.2 1.2 - - - -
106H VAL* 4.5 18.8 - - + -
109H GLN* 3.0 26.7 - - - +
126H TYR* 3.4 27.4 - - + -
129H GLU* 3.5 16.2 - - + +
130H LEU* 3.2 38.1 - - - +
132H THR* 1.3 82.6 + - - +
134H MET* 1.3 63.9 + - + +
135H GLN 3.5 0.2 + - - -
136H HIS* 3.5 22.5 + - - +
137H PHE* 3.9 12.5 + - + -
166H HIS* 4.2 5.6 - - - -
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Residues in contact with MET 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H LEU* 3.0 14.4 + - + +
133H MET* 1.3 76.6 - - + +
135H GLN* 1.3 65.4 + - - +
136H HIS 3.2 2.2 - - - -
137H PHE* 2.9 35.8 + - + +
138H SER* 3.2 7.3 + - - -
162H VAL* 6.2 0.2 - - + -
163H LEU* 4.2 12.3 - - + -
166H HIS* 4.1 28.7 - - + -
173H CYS* 3.8 38.6 - - + +
174H LEU* 3.8 32.8 - - + -
177H PHE* 3.7 12.6 - - + -
180H LEU* 3.8 20.1 - - + +
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Residues in contact with GLN 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PRO 2.8 14.7 + - - +
132H THR* 3.2 25.0 - - - +
133H MET 3.3 0.2 - - - -
134H MET* 1.3 73.9 - - - +
136H HIS* 1.3 65.8 + - - +
138H SER* 2.8 26.9 + - - -
139H GLN* 2.9 27.7 + - - +
177H PHE* 3.5 24.0 - - + -
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Residues in contact with HIS 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LYS* 5.1 10.1 - - - -
50G PHE* 5.4 8.2 - + - -
55G ASP 3.7 10.6 - - - +
56G PHE* 3.4 31.2 - - + -
57G PRO* 4.3 27.7 - - + +
132H THR* 3.1 30.2 + - - -
133H MET* 3.5 14.1 + - - +
134H MET 3.2 0.2 - - - -
135H GLN* 1.3 87.9 + - - +
137H PHE* 1.3 60.7 + - - +
139H GLN* 3.2 24.0 + - - +
140H PHE* 3.0 18.0 + - - +
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Residues in contact with PHE 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G PHE* 3.6 25.1 - + - -
99H LEU* 3.9 20.2 - - + -
102H GLN* 4.8 7.4 - - + -
103H ALA* 4.5 9.2 - - + -
106H VAL* 4.1 39.0 - - + -
133H MET* 4.0 9.4 - - + -
134H MET* 2.9 38.5 + - + +
136H HIS* 1.3 77.3 - - - +
138H SER* 1.3 61.4 + - - +
140H PHE* 3.1 4.7 + - - +
141H LEU* 3.1 19.9 + - - +
147H PHE* 3.5 27.6 - + + -
159H ALA* 6.1 1.6 - - + -
162H VAL* 4.7 9.6 - - + -
163H LEU* 4.9 9.0 - - + -
166H HIS* 6.3 0.4 - + - -
180H LEU* 4.1 12.8 - - + -
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Residues in contact with SER 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H MET 3.2 3.4 + - - -
135H GLN* 2.8 12.0 + - - -
137H PHE* 1.3 79.1 - - - +
139H GLN* 1.3 55.7 + - - +
142H GLY* 3.1 28.2 + - - -
177H PHE* 3.8 25.4 - - - +
178H PRO* 5.6 0.3 - - - +
179H ASN* 2.5 37.9 + - - +
180H LEU* 3.9 8.6 - - - +
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Residues in contact with GLN 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LEU 5.7 2.9 + - - -
55G ASP* 5.1 9.2 - - - +
95H ARG* 5.5 1.0 + - - -
135H GLN* 2.9 30.4 + - - +
136H HIS* 3.3 27.9 - - - +
138H SER* 1.3 78.8 - - - +
140H PHE* 1.3 55.4 + - - +
141H LEU 4.8 1.3 - - - -
142H GLY* 5.5 0.9 - - - -
143H LYS* 5.5 4.2 + - - -
144H ARG* 5.1 2.1 + - - -
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Residues in contact with PHE 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ASP* 3.6 35.4 - - + -
56G PHE* 3.5 27.6 - + + -
95H ARG* 3.0 89.8 + - + +
98H ILE* 4.6 11.2 - - + -
99H LEU* 4.7 4.7 - - + -
136H HIS 3.0 10.6 + - - +
137H PHE 3.1 8.7 + - - +
139H GLN* 1.3 78.4 - - - +
141H LEU* 1.3 55.6 + - - +
144H ARG* 2.7 25.1 + - - -
147H PHE* 3.2 31.9 - + + -
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137H PHE 3.1 13.6 + - - +
139H GLN 4.8 0.7 - - - -
140H PHE* 1.3 74.4 - - - +
142H GLY* 1.3 63.8 + - - +
143H LYS* 3.0 6.9 + - - -
144H ARG* 2.5 50.4 + - - +
145H PRO 4.6 0.4 - - - +
146H TRP* 3.9 1.8 - - - +
147H PHE* 3.5 45.7 - - + +
179H ASN* 3.5 34.1 - - + +
180H LEU* 3.6 20.6 - - + -
183H PHE* 3.8 21.5 - - + -
186H ARG* 4.8 2.9 - - - +
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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