Contacts of the helix formed by residues 133 - 152 (chain H) in PDB entry 1SMK
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 LEU 133 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122H VAL* 3.9 17.5 - - + +
123H PRO 3.9 9.0 - - - +
124H ARG* 3.5 47.3 - - + -
129H THR* 6.1 0.7 - - - +
130H ARG* 3.5 8.4 + - - +
131H ASP* 3.4 18.2 - - - +
132H ASP* 1.3 73.5 - - - +
134H PHE* 1.3 71.3 + - + +
135H LYS 3.0 2.0 - - - -
136H ILE* 2.8 37.3 + - + +
137H ASN* 2.9 19.6 + - - +
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Residues in contact with PHE 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H ASP 4.9 2.2 - - - +
132H ASP* 4.2 11.4 - - - +
133H LEU* 1.3 86.0 - - + +
135H LYS* 1.3 60.4 + - + +
137H ASN* 4.0 4.6 - - - +
138H ALA* 2.5 54.0 + - + +
163H PRO* 3.8 26.0 - - + -
166H SER* 3.5 31.2 - - - -
167H THR* 5.4 0.4 - - + -
170H ILE* 4.2 15.9 - - + -
349H LYS* 3.9 55.2 - - + +
353H PHE* 4.2 16.8 - + + -
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Residues in contact with LYS 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H ARG* 2.9 44.0 - - - +
132H ASP* 3.5 27.7 - - + +
133H LEU 3.0 0.2 - - - -
134H PHE* 1.3 85.5 - - + +
136H ILE* 1.3 54.1 + - + +
138H ALA* 3.8 5.2 - - - +
139H GLY* 2.7 31.2 + - - -
353H PHE* 4.0 16.1 - - + -
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H VAL* 3.5 38.4 - - + -
130H ARG* 6.1 3.1 - - - +
132H ASP 5.3 0.4 - - - +
133H LEU* 2.8 31.7 + - + +
135H LYS* 1.3 73.0 - - + +
137H ASN* 1.3 54.2 + - - +
139H GLY* 2.8 5.4 + - - -
140H ILE* 2.7 43.2 + - + +
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Residues in contact with ASN 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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120H ALA 4.5 3.3 + - - +
121H GLY* 3.5 18.6 - - - -
122H VAL* 2.9 47.0 + - - +
133H LEU* 2.9 17.6 + - + +
134H PHE* 4.0 4.7 - - - +
136H ILE* 1.3 78.3 - - - +
138H ALA* 1.3 62.7 + - - +
140H ILE* 3.3 8.4 + - - +
141H VAL* 2.9 31.0 + - + +
161H SER* 4.8 1.0 - - - +
162H ASN* 3.2 39.2 + - - +
163H PRO* 5.4 0.2 - - + -
167H THR* 5.4 0.2 - - - -
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Residues in contact with ALA 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 PHE* 2.5 39.1 + - + +
137H ASN* 1.3 72.8 - - - +
139H GLY* 1.3 62.9 + - - +
141H VAL* 3.2 6.3 + - - +
142H LYS* 2.9 23.2 + - - +
163H PRO* 6.1 0.6 - - - +
167H THR* 5.2 2.2 - - - -
170H ILE* 3.4 29.7 - - + +
353H PHE* 3.5 21.8 - - + -
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Residues in contact with GLY 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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135H LYS 2.7 19.7 + - - -
136H ILE 2.8 5.0 + - - -
138H ALA* 1.3 73.9 - - - +
140H ILE* 1.3 61.5 + - - -
142H LYS* 3.1 8.2 + - - +
143H THR* 3.0 28.4 + - - +
353H PHE* 3.9 10.0 - - - -
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Residues in contact with ILE 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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120H ALA* 4.0 19.5 - - + +
121H GLY* 4.0 15.3 - - - +
122H VAL* 3.9 28.5 - - + +
136H ILE* 2.7 27.8 + - + +
137H ASN* 3.5 8.5 - - - +
139H GLY* 1.3 70.5 - - - +
141H VAL* 1.3 67.6 + - + +
143H THR* 3.0 20.0 + - - +
144H LEU* 3.0 34.6 + - + +
161H SER* 5.6 0.2 - - - +
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Residues in contact with VAL 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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118H VAL* 6.1 0.9 - - - -
137H ASN 2.9 19.8 + - - +
138H ALA* 3.4 7.2 - - - +
140H ILE* 1.3 76.5 - - + +
142H LYS* 1.3 65.9 + - - +
144H LEU* 2.7 19.7 + - - +
145H CYS* 2.8 31.7 + - - -
159H LEU* 4.2 11.7 - - + -
161H SER* 3.7 31.0 - - - +
167H THR* 3.7 27.6 - - + +
170H ILE* 3.7 18.2 - - + -
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Residues in contact with LYS 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 ALA 2.9 13.1 + - - +
139H GLY* 3.1 11.4 + - - +
141H VAL* 1.3 76.5 - - - +
143H THR* 1.3 68.6 + - + +
145H CYS* 3.2 1.7 + - - +
146H GLU* 3.0 59.9 + - + +
170H ILE* 4.3 1.1 - - + +
174H VAL* 4.3 13.0 - - + -
353H PHE* 4.8 7.2 - - + -
354H ILE* 3.5 32.8 - - + -
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Residues in contact with THR 143 (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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103H GLN* 4.8 14.1 + - - +
106H LEU* 4.2 9.0 - - - +
139H GLY* 3.0 13.2 + - - +
140H ILE* 3.0 18.4 + - - +
142H LYS* 1.3 79.9 - - + +
144H LEU* 1.3 55.9 + - - +
146H GLU* 2.5 37.6 - - - +
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H LEU* 3.9 25.8 - - + -
76H TYR* 4.1 15.3 - - + +
103H GLN* 5.8 1.8 - - - +
106H LEU* 4.1 21.1 - - + -
110H LEU* 4.4 3.6 - - - +
118H VAL* 3.8 16.8 - - + -
120H ALA* 3.5 32.3 - - + -
140H ILE* 3.0 26.3 + - + +
141H VAL* 2.7 19.2 + - - +
143H THR* 1.3 75.7 - - - +
145H CYS* 1.3 62.7 + - - +
146H GLU 3.1 3.8 + - - +
147H GLY* 4.0 1.0 - - - -
148H ILE* 2.9 29.9 + - + +
161H SER* 5.7 0.2 - - - +
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Residues in contact with CYS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H VAL* 2.8 29.0 + - - -
142H LYS 3.8 3.4 - - - +
144H LEU* 1.3 73.7 - - - +
146H GLU* 1.3 58.4 + - - +
148H ILE* 2.9 31.4 + - - +
149H ALA* 2.9 13.0 + - - +
157H VAL* 6.0 2.0 - - - -
159H LEU* 5.2 3.8 - - - -
171H ALA* 3.3 36.6 - - - -
174H VAL* 3.5 23.3 - - + -
175H PHE* 3.3 19.6 - - + -
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Residues in contact with GLU 146 (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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106H LEU* 4.1 3.8 - - - +
142H LYS* 3.0 50.7 + - - +
143H THR* 2.5 38.5 - - - +
144H LEU* 3.4 1.9 - - - +
145H CYS* 1.3 72.6 - - - +
147H GLY* 1.3 57.2 + - - +
148H ILE 3.3 0.2 - - - -
149H ALA* 4.7 4.3 - - - +
174H VAL* 3.6 18.1 - - + +
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Residues in contact with GLY 147 (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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106H LEU* 4.4 6.3 - - - -
110H LEU* 3.2 18.3 - - - +
145H CYS 3.1 0.8 + - - -
146H GLU* 1.3 74.3 - - - +
148H ILE* 1.3 59.2 + - - +
149H ALA* 3.1 4.9 - - - +
150H LYS* 3.4 23.9 - - - +
151H CYS* 2.8 36.8 + - - +
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Residues in contact with ILE 148 (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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50H LEU* 4.3 7.2 - - + -
110H LEU* 4.0 14.8 - - + -
116H ILE* 4.1 34.3 - - + -
118H VAL* 4.4 7.9 - - + -
144H LEU* 2.9 25.0 + - + +
145H CYS* 2.9 22.3 + - - +
147H GLY* 1.3 77.2 - - - +
149H ALA* 1.3 55.2 + - - +
150H LYS 3.2 0.9 - - - -
152H CYS* 3.1 34.0 - - - +
153H PRO* 3.1 3.6 - - + +
155H ALA 5.6 0.2 - - - +
157H VAL* 3.9 24.9 - - + -
175H PHE* 3.7 21.1 - - + -
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Residues in contact with ALA 149 (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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145H CYS 2.9 13.7 + - - +
146H GLU* 4.9 2.9 - - - -
147H GLY 3.1 2.4 - - - +
148H ILE* 1.3 79.0 - - - +
150H LYS* 1.3 57.2 + - - +
153H PRO* 3.7 19.3 - - - +
174H VAL* 5.5 1.1 - - + +
175H PHE* 3.8 12.8 - - + -
178H ALA* 3.8 18.0 - - + +
180H THR* 3.1 32.5 - - - +
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Residues in contact with LYS 150 (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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107H GLU* 3.4 31.5 + - + +
147H GLY* 3.4 20.3 + - - +
148H ILE 3.2 0.2 - - - -
149H ALA* 1.3 81.9 - - - +
151H CYS* 1.3 67.2 + - - +
152H CYS 3.7 0.7 - - - -
153H PRO* 4.5 3.4 - - - +
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Residues in contact with CYS 151 (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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106H LEU* 5.7 0.4 - - - -
107H GLU* 3.3 39.9 - - + -
110H LEU* 3.8 5.8 - - + -
111H THR* 3.3 43.4 - - - +
112H GLY 3.5 4.3 + - - -
147H GLY* 2.8 25.6 + - - +
150H LYS* 1.3 85.4 - - - +
152H CYS* 1.3 64.7 + - - +
153H PRO* 3.9 1.6 - - - -
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Residues in contact with CYS 152 (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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110H LEU* 3.4 29.8 - - - +
112H GLY* 4.5 1.3 - - - +
113H MET* 4.1 8.5 - - - +
116H ILE* 3.2 33.4 - - - -
148H ILE* 3.1 19.1 + - - +
151H CYS* 1.3 81.3 - - - +
153H PRO* 1.3 59.1 - - - +
154H ARG* 2.8 16.9 + - - -
155H ALA* 2.9 24.5 + - + +
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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
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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