Contacts of the strand formed by residues 150 - 162 (chain B) in PDB entry 5M5X
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 GLU 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B TRP* 3.4 1.1 - - + +
144B SER* 3.3 23.2 - - - -
145B VAL* 3.6 19.6 + - + +
149B GLU* 1.3 80.1 - - + +
151B ASN* 1.3 64.2 + - - +
152B LEU* 3.7 23.9 + - + +
440B PHE 5.0 0.3 - - - +
441B LYS* 3.1 41.5 - - - +
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Residues in contact with ASN 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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142B LYS* 3.2 30.9 + - - +
143B TRP 3.2 4.0 - - - +
144B SER* 2.6 28.4 + - - -
148B GLY* 4.0 13.1 + - - -
150B GLU* 1.3 73.7 - - - +
152B LEU* 1.3 64.0 + - - +
153B PHE* 4.0 16.4 + - + -
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Residues in contact with LEU 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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141B LEU* 3.3 2.4 - - - +
143B TRP* 2.9 58.4 + - + +
150B GLU* 3.7 39.9 - - + +
151B ASN* 1.3 77.1 - - - +
153B PHE* 1.3 63.2 + - - +
154B GLU* 5.3 0.9 - - - +
440B PHE 4.8 8.3 - - - +
441B LYS 4.8 12.8 - - - +
442B ASP 5.2 2.2 - - - +
443B LYS* 3.6 37.2 - - + +
446B MET* 6.1 5.2 - - + -
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Residues in contact with PHE 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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100B GLU* 3.5 28.9 - - - +
140B LYS* 5.1 14.6 - - + -
141B LEU 3.4 7.0 - - - +
142B LYS* 3.6 35.2 - - + -
151B ASN* 4.0 16.7 + - + -
152B LEU* 1.3 80.0 - - - +
154B GLU* 1.3 64.9 + - - +
155B VAL* 6.0 2.0 - - + -
443B LYS* 3.8 10.4 + - - +
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Residues in contact with GLU 154 (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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140B LYS* 3.5 0.7 - - - +
141B LEU* 2.9 45.9 + - + +
152B LEU 5.3 0.7 - - - +
153B PHE* 1.3 78.0 - - - +
155B VAL* 1.3 69.1 + - - +
156B ARG* 3.0 42.7 - - - +
443B LYS* 4.3 16.4 - - - +
446B MET* 5.9 7.2 - - + -
447B SER* 6.1 1.1 - - - +
450B LEU* 4.9 4.1 - - - +
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Residues in contact with VAL 155 (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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138B LEU* 4.5 17.7 - - + -
139B LEU 3.2 18.4 - - - +
140B LYS* 3.7 23.1 - - + -
153B PHE* 6.0 1.6 - - + -
154B GLU* 1.3 82.9 - - - +
156B ARG* 1.3 72.9 + - - +
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Residues in contact with ARG 156 (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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138B LEU* 3.7 6.4 - - - +
139B LEU* 3.0 34.8 + - - +
141B LEU* 5.1 7.3 - - + +
154B GLU* 3.0 38.5 + - - +
155B VAL* 1.3 72.1 - - - +
157B ASP* 1.3 75.3 + - - +
158B CYS* 4.8 2.4 - - - -
450B LEU* 3.2 36.1 + - - +
451B MET* 5.3 7.7 + - - +
455B GLU* 3.4 41.8 + - - +
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Residues in contact with ASP 157 (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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136B LYS* 4.4 21.6 - - + +
137B LEU 3.1 14.8 - - - +
138B LEU* 3.7 13.6 - - + +
156B ARG* 1.3 95.1 + - - +
158B CYS* 1.3 68.2 + - - +
159B GLY* 4.5 6.2 + - - +
455B GLU* 4.8 0.7 - - - +
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Residues in contact with CYS 158 (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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137B LEU* 3.2 16.4 + - + -
139B LEU* 3.6 23.8 - - - -
156B ARG* 4.8 4.3 - - - -
157B ASP* 1.3 80.3 - - - +
159B GLY* 1.3 58.2 + - - +
420B TYR* 4.4 11.4 - - - -
455B GLU* 3.4 38.6 - - - +
456B ASN* 3.7 3.4 - - - +
457B ILE* 2.9 46.7 + - + +
458B GLY 3.4 0.2 + - - -
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Residues in contact with GLY 159 (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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135B GLY 4.6 0.2 - - - -
136B LYS* 3.7 8.3 - - - +
137B LEU* 3.2 25.3 + - - +
157B ASP* 3.8 8.1 + - - +
158B CYS* 1.3 78.2 - - - +
160B GLY* 1.3 60.5 + - - -
161B LEU* 3.9 1.9 + - - -
456B ASN* 4.3 10.3 - - - -
458B GLY* 4.4 2.7 - - - -
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Residues in contact with GLY 160 (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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134B ARG* 3.5 31.0 - - - +
135B GLY 3.2 17.0 - - - -
159B GLY* 1.3 72.2 - - - -
161B LEU* 1.3 64.9 + - - -
162B PRO* 3.8 4.5 - - - +
458B GLY* 3.5 19.5 - - - +
462B GLN* 5.2 1.0 - - - +
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Residues in contact with LEU 161 (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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104B ILE* 5.1 10.5 - - + -
134B ARG* 3.6 1.6 - - - -
135B GLY* 2.7 33.6 + - - +
136B LYS* 5.0 0.2 - - - +
137B LEU* 3.7 32.8 - - + +
159B GLY 3.9 3.1 + - - +
160B GLY* 1.3 76.3 - - - -
162B PRO* 1.3 64.3 - - + +
163B VAL* 3.3 6.3 - - + +
409B TYR* 3.3 19.1 - - + +
413B LEU* 3.7 36.6 - - + -
457B ILE* 3.7 24.2 - - + -
458B GLY* 4.1 7.0 - - - -
461B MET* 3.8 15.7 - - + -
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Residues in contact with PRO 162 (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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132B SER* 5.0 0.7 - - - -
133B TYR 3.3 15.0 - - - +
134B ARG* 3.8 4.0 - - + -
160B GLY 3.8 7.4 - - - +
161B LEU* 1.3 82.9 - - + +
163B VAL* 1.3 60.2 + - - +
164B MET 4.4 0.2 + - - -
194B PHE* 4.7 10.1 - - + -
195B ILE 4.2 14.4 - - - +
196B VAL* 6.2 0.9 - - + -
409B TYR* 2.7 36.5 + - + +
458B GLY 4.8 7.0 - - - +
461B MET* 5.0 5.4 - - + +
462B GLN* 3.8 25.6 - - - +
465B LEU* 3.6 28.5 - - + -
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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
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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