Contacts of the helix formed by residues 135 - 146 (chain B) in PDB entry 5SWW
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 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B PHE* 3.2 42.9 - - + +
103B SER* 3.3 20.0 - - - +
133B ASP* 3.0 7.4 + - - +
134B PRO* 1.3 91.5 - - + +
136B TYR* 1.3 63.8 + - - +
137B LYS 3.2 2.7 - - - -
138B GLU* 3.2 27.9 + - + +
139B ALA 3.1 15.4 + - - -
63D LEU* 4.6 11.7 - - + -
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Residues in contact with TYR 136 (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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99B SER* 5.0 5.2 - - - +
100B PRO 5.3 2.5 - - - +
101B CYS* 5.8 0.4 - - - +
129B ILE* 3.5 26.5 - - + -
130B TYR* 3.2 22.2 - - + +
131B ASP* 3.6 25.0 - - + +
133B ASP* 3.1 26.2 + - + +
134B PRO* 4.3 8.5 - - + -
135B LEU* 1.3 74.7 - - - +
137B LYS* 1.3 103.5 + - + +
139B ALA* 3.0 10.5 + - - +
140B LEU* 2.9 29.0 + - + +
189B ARG* 3.9 11.6 + - - -
193B ILE* 3.6 26.4 - - + +
60D LYS* 4.5 12.9 + - + +
62D LEU* 5.7 7.0 - - + -
104D TRP* 5.8 0.9 + - - -
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Residues in contact with LYS 137 (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 PRO 5.3 0.9 + - - +
135B LEU 3.2 0.8 - - - -
136B TYR* 1.3 117.4 - - + +
138B GLU* 1.3 67.0 + - - +
140B LEU* 3.4 1.6 + - - +
141B GLN* 2.9 45.1 + - - +
193B ILE* 3.9 33.4 - - + +
60D LYS* 5.8 4.3 - - - +
62D LEU* 6.2 5.4 - - + +
132D TYR* 5.5 5.1 + - - -
2H G 4.4 15.8 + - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.3 17.7 - - + -
134B PRO 4.5 1.0 - - - +
135B LEU* 3.2 45.1 + - + +
137B LYS* 1.3 85.5 - - - +
139B ALA* 1.3 57.3 + - - +
141B GLN* 4.1 12.7 - - - +
142B MET* 2.9 32.7 + - + +
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Residues in contact with ALA 139 (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 PRO* 3.3 26.7 - - + +
101B CYS 3.6 16.8 - - - +
102B PHE* 3.6 14.1 - - + +
107B ALA* 3.9 11.9 - - + +
135B LEU 3.1 5.7 + - - +
136B TYR* 3.0 10.8 + - - +
138B GLU* 1.3 73.6 - - - +
140B LEU* 1.3 60.5 + - - +
142B MET* 3.3 2.6 + - - +
143B LEU* 2.9 35.5 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.7 27.6 - - - +
100B PRO* 4.9 3.4 - - + +
129B ILE* 4.6 11.4 - - + -
136B TYR* 2.9 27.7 + - + +
137B LYS 4.0 2.2 - - - +
139B ALA* 1.3 75.0 - - + +
141B GLN* 1.3 58.0 + - - +
143B LEU* 3.3 14.5 + - + +
144B ARG* 2.9 28.1 + - - +
150B VAL* 3.8 25.7 - - + +
152B ILE* 6.5 0.9 - - + -
190B LEU* 3.6 28.0 - - + -
193B ILE* 3.9 24.7 - - + -
194B LEU* 3.9 7.5 - - + +
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Residues in contact with GLN 141 (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 LYS* 2.9 30.4 + - - +
138B GLU* 4.1 12.3 - - - +
140B LEU* 1.3 75.3 - - - +
142B MET* 1.3 57.3 + - - +
144B ARG* 3.2 24.6 + - - +
145B ASP* 2.8 40.5 + - - +
193B ILE* 3.1 28.1 + - + +
194B LEU* 3.9 18.2 - - + -
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Residues in contact with MET 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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102B PHE* 3.6 27.6 - - + -
107B ALA* 3.9 12.3 - - + +
108B GLY* 3.8 26.7 - - - -
111B ARG* 3.4 52.9 - - + +
138B GLU* 2.9 22.1 + - + +
139B ALA* 3.6 4.5 - - - +
141B GLN* 1.3 76.3 - - - +
143B LEU* 1.3 62.7 + - - +
145B ASP* 3.4 7.6 + - - +
146B ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 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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100B PRO* 3.7 36.3 - - + +
107B ALA* 4.3 16.4 - - + +
110B VAL* 3.7 35.9 - - + -
111B ARG* 5.1 2.2 - - - +
114B LEU* 5.5 0.7 - - + -
124B ILE* 3.7 16.2 - - + -
139B ALA 2.9 21.9 + - - +
140B LEU* 3.5 13.7 - - + +
142B MET* 1.3 76.8 - - - +
144B ARG* 1.3 60.8 + - - +
146B ALA* 3.3 8.7 + - - +
148B ALA* 3.2 33.9 + - + +
150B VAL* 3.8 13.9 - - + -
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Residues in contact with ARG 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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140B LEU 2.9 13.8 + - - +
141B GLN* 3.6 28.6 + - - +
143B LEU* 1.3 77.9 - - - +
145B ASP* 1.3 84.0 + - - +
146B ALA 3.1 1.6 + - - -
147B GLY* 3.1 14.2 + - - -
148B ALA 3.5 12.6 + - - +
150B VAL* 3.8 7.8 - - + +
194B LEU* 3.3 59.6 + - + +
195B GLN 3.7 9.3 - - - +
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Residues in contact with ASP 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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111B ARG* 6.0 1.1 - - - -
141B GLN* 2.8 27.1 + - - +
142B MET* 3.8 6.3 - - - +
143B LEU 3.4 0.2 - - - -
144B ARG* 1.3 100.2 + - - +
146B ALA* 1.3 58.5 + - - +
147B GLY 3.4 1.4 + - - -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ARG* 3.7 31.6 - - + +
114B LEU* 4.0 29.0 - - + +
115B GLN* 5.5 7.3 - - + +
142B MET 3.1 15.7 + - - +
143B LEU* 3.8 7.2 - - + +
144B ARG 3.1 1.6 - - - -
145B ASP* 1.3 77.0 - - - +
147B GLY* 1.3 59.1 + - - +
148B ALA 3.4 1.3 + - - -
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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