Contacts of the helix formed by residues 137 - 153 (chain B) in PDB entry 3SJ5
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 MET 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 4.0 15.3 - - + -
9B TRP* 3.7 12.6 - - + -
67B TRP* 3.5 44.9 - - + -
131B TYR* 2.9 19.9 + - - +
135B ARG* 3.6 19.3 - - + +
136B LYS* 1.3 72.2 - - - +
138B TYR* 1.3 62.6 + - - +
139B ASP 3.3 2.9 - - - -
140B TYR* 3.3 26.0 + - + -
141B PHE* 3.1 21.8 + - - +
502B HEM 3.6 32.3 - - + +
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU 5.0 2.0 - - - -
161A VAL* 5.0 2.9 - - - -
131B TYR* 4.0 10.8 - + - -
136B LYS* 3.2 31.9 + - + +
137B MET* 1.3 76.7 - - - +
139B ASP* 1.3 63.0 + - - +
141B PHE* 3.4 6.0 - - - +
142B LEU* 3.0 32.8 + - - +
163B ARG* 3.4 44.4 - - + +
164B GLY 3.5 12.8 + - - -
165B GLU* 2.6 26.3 + - - -
170B SER* 3.4 19.1 - - - -
171B ARG 3.8 15.7 - - - -
172B LEU* 3.7 30.9 - - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 3.2 59.2 - - - +
67B TRP* 4.0 9.0 - - + -
68B ARG* 3.4 33.4 + - + +
137B MET 3.3 0.4 - - - -
138B TYR* 1.3 80.5 - - - +
140B TYR* 1.3 61.1 + - - +
142B LEU* 3.4 8.8 + - - +
143B GLY 2.9 24.1 + - - -
163B ARG* 5.0 7.9 + - - -
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 6.2 0.2 - - - -
9B TRP* 3.1 24.7 + + - -
67B TRP* 3.7 34.1 - + + +
70B VAL* 4.2 2.2 - - + -
71B GLY* 3.6 27.5 - - - -
74B ASN* 2.6 33.7 + - - -
78B PHE* 4.1 12.5 - - - -
137B MET* 3.3 29.9 + - + +
139B ASP* 1.3 76.7 - - - +
141B PHE* 1.3 55.4 + - - +
143B GLY* 3.2 1.6 + - - -
144B LEU* 2.9 52.8 + - + +
502B HEM 3.6 41.1 - + + +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.8 24.5 - - + -
129B MET* 4.2 16.6 - - + -
131B TYR* 3.8 39.0 - + + -
137B MET 3.1 12.9 + - - +
138B TYR* 3.4 7.2 - - - +
140B TYR* 1.3 77.3 - - - +
142B LEU* 1.3 65.8 + - + +
144B LEU* 3.3 7.8 + - - +
145B ILE* 3.2 49.2 + - + +
172B LEU* 4.0 24.7 - - + -
174B VAL* 4.3 19.7 - - + -
502B HEM 3.7 34.7 - - + +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.7 35.4 - - - +
138B TYR 3.0 21.6 + - - +
139B ASP* 3.9 10.1 - - - +
140B TYR 3.4 0.2 - - - -
141B PHE* 1.3 84.4 - - + +
143B GLY* 1.3 62.4 + - - +
145B ILE* 3.3 9.5 + - + +
146B GLU* 3.2 26.6 + - - +
158B VAL* 4.4 13.5 - - + -
160B GLU* 3.7 20.4 - - - +
163B ARG* 4.2 10.1 - - - +
172B LEU* 4.0 14.4 - - + -
174B VAL* 3.9 27.6 - - + -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.4 31.1 - - - +
71B GLY 3.5 6.3 - - - -
72B ARG* 3.4 15.0 - - - +
139B ASP 2.9 12.7 + - - -
140B TYR 3.6 2.9 - - - -
142B LEU* 1.3 74.7 - - - +
144B LEU* 1.3 58.8 + - - +
146B GLU* 3.2 2.4 + - - -
147B GLY 2.8 25.1 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLY* 3.3 22.6 - - - +
74B ASN* 3.9 17.3 - - + -
75B ILE* 3.5 20.2 - - + +
78B PHE* 5.1 4.3 - - + -
140B TYR* 2.9 48.3 + - + +
141B PHE* 3.3 4.5 + - - +
143B GLY* 1.3 72.5 - - - +
145B ILE* 1.3 64.4 + - - +
147B GLY 3.4 0.2 + - - -
148B SER* 2.9 29.8 + - - -
502B HEM 3.3 55.6 - - + +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 5.4 0.3 - - - +
95B LEU* 4.8 8.2 - - + +
129B MET* 4.5 3.1 - - - -
141B PHE* 3.2 45.7 + - + +
142B LEU* 3.6 13.2 - - + +
143B GLY 3.3 0.2 - - - -
144B LEU* 1.3 76.6 - - - +
146B GLU* 1.3 62.5 + - - +
148B SER* 3.1 17.8 + - - -
149B SER* 3.1 12.6 + - - -
156B ILE* 3.6 24.1 - - + +
158B VAL* 4.1 15.0 - - + -
174B VAL* 4.2 15.0 - - + -
176B ILE* 4.2 16.4 - - + -
502B HEM 3.4 21.1 - - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 3.0 35.1 + - - +
72B ARG* 2.9 41.5 + - + +
142B LEU 3.2 10.1 + - - +
143B GLY 3.2 5.8 + - - +
145B ILE* 1.3 79.6 - - + +
147B GLY* 1.3 61.9 + - - +
149B SER* 3.3 9.2 + - - -
150B LYS* 3.2 32.3 + - - +
156B ILE* 5.0 2.7 - - + -
158B VAL* 5.3 11.0 - - + +
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.8 24.6 - - - +
75B ILE* 3.7 12.2 - - - +
143B GLY 2.8 15.9 + - - -
144B LEU 3.8 1.8 - - - -
146B GLU* 1.3 76.7 - - - +
148B SER* 1.3 57.7 + - - +
150B LYS* 3.4 9.8 + - - +
151B PHE* 3.0 28.6 + - - +
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Residues in contact with SER 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 3.4 17.8 - - - +
91B LEU* 3.7 19.5 - - - -
94B PHE* 3.4 26.7 - - - -
95B LEU* 4.5 3.6 - - - -
144B LEU 2.9 17.5 + - - -
145B ILE* 3.1 10.7 + - - -
147B GLY* 1.3 74.0 - - - +
149B SER* 1.3 64.8 + - - +
151B PHE* 4.4 1.1 - - - +
152B PHE* 3.0 33.4 + - - +
502B HEM 3.7 4.7 - - - +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 3.8 9.3 - - - +
145B ILE 3.1 5.4 + - - -
146B GLU* 3.5 11.2 - - - -
148B SER* 1.3 78.0 - - - +
150B LYS* 1.3 63.3 + - - +
153B LYS* 3.0 18.5 + - - -
154B GLU 2.7 35.2 + - - -
155B GLU* 4.0 2.1 - - - -
156B ILE* 3.8 35.4 + - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B ARG* 3.9 29.8 - - + +
146B GLU* 3.2 18.6 + - - +
147B GLY* 3.7 10.8 - - - +
148B SER 3.2 0.2 - - - -
149B SER* 1.3 81.9 - - - +
151B PHE* 1.3 63.2 + - - +
153B LYS* 3.2 20.4 + - - +
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Residues in contact with PHE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 3.9 17.9 - - + -
76B LYS* 4.8 11.2 - - + -
79B SER* 3.3 35.9 - - - -
86B PHE* 3.5 34.1 - + + -
147B GLY 3.0 17.1 + - - +
148B SER* 3.3 3.3 + - - +
150B LYS* 1.3 76.6 - - - +
152B PHE* 1.3 75.3 + + + +
153B LYS* 3.2 13.1 + - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.8 37.5 - + - -
89B ARG* 3.1 34.1 - - + -
90B ARG 4.2 2.2 - - - -
91B LEU* 3.8 26.0 - - + -
94B PHE* 3.5 47.6 - + + -
148B SER* 3.0 27.8 + - - +
149B SER 4.4 1.1 - - - +
151B PHE* 1.3 84.4 - + - +
153B LYS* 1.3 71.1 + - - +
154B GLU* 3.3 21.0 + - + +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B SER 3.0 8.9 + - - -
150B LYS* 3.2 12.6 + - - +
151B PHE* 3.2 10.6 + - - +
152B PHE* 1.3 80.6 - - - +
154B GLU* 1.3 60.5 + - - +
155B GLU* 4.2 1.2 + - - -
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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
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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