Contacts of the helix formed by residues 125 - 146 (chain H) in PDB entry 1R5I
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 ASN 125 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H LEU* 3.6 19.3 - - + +
70H LEU* 5.4 4.9 - - - +
71H GLU* 4.2 9.0 + - - +
121H PHE 3.2 14.3 + - - +
122H ILE 3.0 13.0 + - - +
124H GLN* 1.3 77.1 - - - +
126H LYS* 1.3 66.7 + - - +
127H ASN* 3.6 8.3 + - - +
128H PHE* 2.7 45.8 + - + +
129H GLN* 3.2 8.8 + - - +
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Residues in contact with LYS 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H SER 4.6 1.7 + - - +
124H GLN 3.6 4.8 + - - -
125H ASN* 1.3 71.7 - - - +
127H ASN* 1.3 67.8 + - - +
129H GLN* 3.1 19.0 + - + +
130H GLU* 3.1 59.9 + - + +
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Residues in contact with ASN 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H ASN* 3.2 7.0 + - - +
126H LYS* 1.3 84.0 - - - +
128H PHE* 1.3 63.6 + - - +
130H GLU* 3.1 21.4 + - - +
131H LEU* 3.0 44.5 + - - +
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Residues in contact with PHE 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 4.8 2.2 - - + -
65H ASP 4.9 0.2 - - - -
66H TYR* 3.9 28.3 - + - -
68H GLY* 3.1 38.8 - - - -
69H LEU* 3.8 27.4 - - + -
122H ILE* 4.6 16.4 - - + -
125H ASN* 2.7 35.2 + - + +
127H ASN* 1.3 74.8 + - - +
129H GLN* 1.3 60.5 + - - +
131H LEU* 3.2 5.8 + - - +
132H TRP* 2.8 55.9 + + + +
178H TRP* 3.6 24.0 - + - -
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Residues in contact with GLN 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H SER* 2.9 28.6 + - - +
1H MET* 3.6 24.8 + - + +
3H LEU* 5.5 2.4 - - - +
122H ILE* 2.7 45.9 + - + +
123H SER* 3.4 21.8 + - - +
125H ASN 3.2 8.1 + - - +
126H LYS* 3.1 15.0 + - + +
128H PHE* 1.3 77.4 - - - +
130H GLU* 1.3 58.1 + - + +
132H TRP 3.4 0.2 + - - -
133H ASP* 2.9 37.4 + - - +
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Residues in contact with GLU 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LYS* 3.1 50.6 + - + +
127H ASN* 3.6 18.9 + - - +
129H GLN* 1.3 76.7 - - + +
131H LEU* 1.3 63.3 + - + +
133H ASP* 3.4 6.2 + - - +
134H LYS* 2.9 24.1 + - - +
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Residues in contact with LEU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ASN* 3.0 38.0 + - - +
128H PHE* 3.7 6.1 - - - +
130H GLU* 1.3 78.8 - - + +
132H TRP* 1.3 62.0 + - - +
134H LYS* 3.1 9.3 + - + +
135H ALA* 3.0 18.7 + - - +
172H ASN* 3.5 37.5 - - - +
176H LEU* 3.9 22.2 - - + -
178H TRP* 3.6 24.9 - - + -
179H PHE* 3.4 16.1 - - + -
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Residues in contact with TRP 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.0 50.0 - - + -
2H LYS* 5.5 7.0 - - + -
65H ASP* 3.3 22.3 + - - -
66H TYR* 4.1 17.1 - + - -
128H PHE* 2.8 41.4 + + + +
131H LEU* 1.3 71.9 - - - +
133H ASP* 1.3 65.8 + - - +
135H ALA* 3.0 17.7 + - - +
136H VAL* 3.1 32.4 + - + +
178H TRP* 4.1 6.0 - + - -
182H LEU* 3.9 21.0 - - + +
205H ASP* 3.7 13.5 - - + -
206H PHE* 3.4 48.2 - + + -
209H ALA* 3.8 11.2 - - + -
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Residues in contact with ASP 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0H SER* 3.3 31.7 - - - +
1H MET* 3.8 22.9 - - - +
129H GLN* 2.9 21.3 + - - +
130H GLU* 3.7 6.3 - - - +
132H TRP* 1.3 79.5 - - - +
134H LYS* 1.3 58.3 + - - +
136H VAL* 3.0 11.7 + - - +
137H LYS* 2.8 26.8 + - - +
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Residues in contact with LYS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H GLU 2.9 14.4 + - - +
131H LEU* 3.1 12.5 + - + +
133H ASP* 1.3 77.0 - - - +
135H ALA* 1.3 61.6 + - - +
137H LYS* 3.0 15.2 + - + +
138H LEU* 3.0 38.4 + - + +
170H ASP* 2.9 32.4 + - - -
172H ASN* 2.9 32.5 - - - +
179H PHE* 3.8 14.6 - - + -
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Residues in contact with ALA 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H LEU 3.0 12.6 + - - +
132H TRP 3.0 9.6 + - - +
134H LYS* 1.3 76.1 - - - +
136H VAL* 1.3 56.1 + - - +
138H LEU* 3.7 0.6 + - - +
139H THR* 2.6 33.4 + - - -
179H PHE* 3.8 12.1 - - + -
182H LEU* 3.7 30.7 - - + -
183H LEU* 3.9 24.1 - - + +
206H PHE* 4.2 3.8 - - + -
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Residues in contact with VAL 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H TRP* 3.1 41.5 + - + +
133H ASP* 3.0 10.9 + - - +
135H ALA* 1.3 75.0 - - - +
137H LYS* 1.3 68.1 + - - +
139H THR* 3.1 2.9 + - - -
140H LYS* 3.0 36.8 + - - +
206H PHE* 3.9 18.6 - - + -
209H ALA* 3.8 26.9 - - + +
210H VAL* 3.9 12.8 - - + -
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Residues in contact with LYS 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H ASP 2.8 12.0 + - - +
134H LYS* 3.3 18.6 - - + +
136H VAL* 1.3 79.2 - - - +
138H LEU* 1.3 70.0 + - + +
140H LYS* 3.2 11.1 + - - +
141H GLU* 3.0 51.7 + - + +
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H LYS* 3.0 41.9 + - + +
135H ALA 4.1 2.9 - - - +
137H LYS* 1.3 82.2 - - + +
139H THR* 1.3 61.2 + - - +
141H GLU* 3.1 22.0 + - - +
142H MET* 2.8 30.1 + - - +
167H PHE* 3.3 46.8 - - + -
170H ASP* 4.6 6.3 - - - +
179H PHE* 4.1 21.3 - - + -
183H LEU* 4.3 10.3 - - + -
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Residues in contact with THR 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H ALA 2.6 23.1 + - - -
136H VAL 3.1 5.0 + - - -
138H LEU* 1.3 76.5 - - - +
140H LYS* 1.3 56.4 + - - +
142H MET* 3.2 16.6 + - + +
143H LYS* 2.8 26.5 + - - +
183H LEU* 4.1 13.7 - - - +
186H GLY* 3.8 27.6 - - - +
189H LEU* 5.5 0.9 - - + -
190H ILE* 3.7 6.8 - - + +
206H PHE* 3.4 16.0 - - + -
210H VAL* 3.9 24.9 - - + -
211H PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H VAL* 3.0 26.7 + - + +
137H LYS* 3.4 11.4 - - - +
139H THR* 1.3 75.1 - - - +
141H GLU* 1.3 66.7 + - + +
143H LYS* 2.9 27.8 + - + +
144H ILE* 3.3 11.4 + - - +
209H ALA 3.7 14.7 + - - -
210H VAL* 2.7 40.8 + - + +
212H GLU 4.1 2.3 + - - -
213H ASP* 3.2 30.3 + - - -
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Residues in contact with GLU 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 LYS* 3.0 41.7 + - + +
138H LEU* 3.1 19.5 + - - +
140H LYS* 1.3 78.2 - - + +
142H MET* 1.3 59.6 + - - +
144H ILE* 3.0 15.0 + - - +
145H LYS* 2.9 31.9 + - + +
167H PHE* 4.0 16.8 - - + -
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Residues in contact with MET 142 (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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138H LEU 2.8 10.9 + - - +
139H THR* 3.4 26.0 - - + +
141H GLU* 1.3 74.3 - - - +
143H LYS* 1.3 65.0 + - - +
145H LYS* 3.9 8.1 - - - -
146H LEU* 3.1 41.6 + - + +
162H LYS* 5.5 2.0 - - - -
163H VAL* 4.9 10.8 - - - -
166H LEU* 3.8 16.4 - - + -
167H PHE* 4.2 22.8 - - + -
183H LEU* 3.3 33.4 - - + +
186H GLY 4.2 0.7 - - - -
187H VAL* 3.6 28.0 - - + +
190H ILE* 4.4 2.7 - - + -
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Residues in contact with LYS 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H THR 2.8 8.7 + - - +
140H LYS* 3.0 20.9 - - + +
142H MET* 1.3 79.4 - - - +
144H ILE* 1.3 56.8 + - + +
147H LYS 4.0 0.9 + - - -
190H ILE* 3.3 29.6 - - + -
193H TYR* 3.4 42.9 + - + -
194H TYR* 2.4 40.1 + - - +
210H VAL* 5.3 5.8 + - + +
211H PHE* 4.1 25.8 - - + +
213H ASP* 5.1 9.1 + - - -
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Residues in contact with ILE 144 (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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140H LYS 3.6 13.5 - - - +
141H GLU* 3.0 10.7 + - - +
143H LYS* 1.3 79.5 - - + +
145H LYS* 1.3 57.4 + - - +
146H LEU 3.1 1.6 - - - -
147H LYS* 2.6 42.2 + - + +
194H TYR* 4.3 2.2 - - - -
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Residues in contact with LYS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H GLU* 2.9 23.3 + - + +
142H MET* 4.0 8.7 - - - +
144H ILE* 1.3 73.0 - - - +
146H LEU* 1.3 58.2 + - - +
147H LYS* 3.3 3.5 + - - +
148H GLY 5.1 0.3 + - - -
149H GLN* 4.4 11.8 - - - +
162H LYS* 6.0 2.2 - - - +
166H LEU* 3.6 41.1 - - + +
167H PHE* 6.3 1.6 - - + -
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Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H MET* 3.1 41.1 + - + +
143H LYS 4.6 2.0 - - - +
144H ILE 2.9 0.2 + - - -
145H LYS* 1.3 74.7 - - - +
147H LYS* 1.3 64.6 + - - +
148H GLY 3.2 3.7 + - - -
149H GLN* 3.4 22.2 + - + +
151H LEU* 3.6 38.6 - - + +
162H LYS* 3.5 39.5 - - + -
166H LEU* 5.1 2.7 - - + -
187H VAL* 4.3 17.5 - - + -
190H ILE* 4.5 15.5 - - + -
194H TYR* 3.4 12.1 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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