Contacts of the helix formed by residues 148 - 157 (chain B) in PDB entry 5SVE
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 SER 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.4 3.1 - - - -
104B GLY 4.3 2.2 - - - -
105B TYR* 3.7 30.0 - - - -
142B ASP* 5.9 1.8 - - - -
146B ARG 3.9 1.2 + - - -
147B ILE* 1.3 75.8 - - - +
149B PHE* 1.3 60.1 + - - +
150B GLU* 3.7 8.0 + - - +
151B GLU* 2.8 37.8 + - - +
152B PHE* 3.0 26.7 + - - +
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Residues in contact with PHE 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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88B GLU* 4.1 19.5 - - + -
91B LEU* 3.9 6.7 - - + -
92B ARG* 3.2 74.7 - - + +
95B PHE* 3.5 37.3 - + + -
104B GLY 4.3 3.3 + - - +
148B SER* 1.3 75.7 - - - +
150B GLU* 1.3 66.5 + - + +
152B PHE* 3.5 1.7 - + - +
153B CYS* 3.0 53.1 + - - -
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Residues in contact with GLU 150 (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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148B SER* 3.3 8.4 + - - +
149B PHE* 1.3 83.1 - - + +
151B GLU* 1.3 60.9 + - + +
153B CYS* 3.5 5.1 + - - +
154B ALA* 3.0 28.9 + - - +
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Residues in contact with GLU 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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139B ALA* 3.6 23.0 - - - +
140B ASP* 3.2 5.3 - - - +
141B LYS* 3.2 18.8 + - + +
142B ASP* 2.5 20.0 + - - +
146B ARG 3.1 4.2 - - - +
147B ILE* 3.3 11.3 - - + +
148B SER* 2.8 32.2 + - - +
150B GLU* 1.3 77.0 - - + +
152B PHE* 1.3 61.2 + - - +
154B ALA* 3.6 10.3 + - - +
155B VAL* 3.3 23.2 + - - +
202B CA 2.4 31.6 - - - -
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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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350A PHE* 3.5 43.5 - + + -
354A LEU* 4.3 17.9 - - + -
91B LEU* 3.7 25.6 - - + -
94B ALA* 4.3 2.9 - - + -
95B PHE* 3.7 36.1 - + + -
98B TYR* 4.2 9.9 - + - -
106B ILE* 4.3 0.4 - - + -
147B ILE* 3.8 7.2 - - + +
148B SER 3.0 19.3 + - - +
149B PHE* 3.5 4.7 - + - +
151B GLU* 1.3 76.0 - - - +
153B CYS* 1.3 76.9 + - - +
155B VAL* 3.0 16.4 + - - +
156B VAL* 3.2 40.5 + - + +
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Residues in contact with CYS 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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91B LEU* 4.2 22.7 - - + -
149B PHE* 3.0 55.5 + - - +
150B GLU* 4.0 4.9 - - - +
152B PHE* 1.3 81.9 - - - +
154B ALA* 1.3 58.5 + - - +
155B VAL 3.0 0.4 - - - -
156B VAL* 4.5 1.3 - - - -
157B GLY* 2.8 34.1 + - - +
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Residues in contact with ALA 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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141B LYS* 6.4 3.4 - - + -
150B GLU 3.0 18.4 + - - +
151B GLU* 3.7 11.0 - - - +
152B PHE 3.2 0.2 - - - -
153B CYS* 1.3 75.3 - - - +
155B VAL* 1.3 61.7 + - + +
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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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348A ASP* 3.5 35.7 - - - +
350A PHE* 4.4 9.2 - - + -
351A THR* 3.9 8.5 + - - +
135B THR* 6.2 0.2 - - + -
139B ALA* 3.9 25.6 - - + +
151B GLU 3.3 17.5 - - - +
152B PHE* 3.0 8.3 + - - +
154B ALA* 1.3 83.9 - - + +
156B VAL* 1.3 64.8 + - + +
157B GLY 3.7 0.4 - - - -
158B GLY 5.2 0.7 + - - -
159B LEU* 5.0 4.0 - - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE* 3.7 42.2 - - + +
351A THR* 4.0 3.4 - - - +
354A LEU* 3.6 21.8 - - + +
91B LEU* 4.9 7.8 - - + +
152B PHE* 3.2 43.9 + - + +
153B CYS* 4.5 1.1 - - - -
155B VAL* 1.3 82.1 - - + +
157B GLY* 1.3 60.1 + - - +
158B GLY 2.8 12.3 + - - -
159B LEU* 3.0 31.7 + - + +
160B ASP 4.6 1.2 + - - -
161B ILE* 5.4 0.3 + - - +
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Residues in contact with GLY 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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87B LYS* 3.0 29.1 + - - -
91B LEU* 4.4 20.6 - - - -
153B CYS* 2.8 21.9 + - - -
154B ALA 4.8 0.2 - - - -
155B VAL 3.7 1.0 - - - -
156B VAL* 1.3 77.3 - - - +
158B GLY* 1.3 55.0 + - - +
159B LEU 3.6 0.4 - - - -
160B ASP* 4.8 1.9 - - - +
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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