Contacts of the helix formed by residues 157 - 167 (chain B) in PDB entry 6V3O
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 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B VAL* 4.6 0.2 - - - -
155B GLY 4.1 1.0 + - - -
156B LYS* 1.3 74.3 - - - +
158B PRO* 1.3 69.5 - - - +
159B GLU* 3.0 21.0 + - - +
160B GLU* 2.5 51.8 + - - +
161B VAL* 3.1 21.6 + - - +
160F GLU* 5.2 9.0 - - - -
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Residues in contact with PRO 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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151B VAL* 4.0 24.2 - - + -
157B SER* 1.3 86.2 - - - +
159B GLU* 1.3 69.4 + - - +
161B VAL* 3.2 3.5 + - + +
162B PHE* 2.9 30.5 + - - +
270B ILE* 3.5 38.8 - - + +
271B GLY 5.4 1.1 - - - -
272B ILE* 3.9 18.8 - - + +
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Residues in contact with GLU 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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157B SER* 3.0 20.5 + - - +
158B PRO* 1.3 92.1 - - - +
160B GLU* 1.3 56.5 + - + +
162B PHE* 3.5 4.9 + - - +
163B GLU* 3.0 31.0 + - - +
272B ILE* 4.3 16.6 - - + +
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Residues in contact with GLU 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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156B LYS* 3.2 39.7 + - + +
157B SER* 2.5 45.3 + - - +
159B GLU* 1.3 73.2 - - + +
161B VAL* 1.3 58.5 + - - +
163B GLU* 3.4 6.5 + - - +
164B ALA* 2.9 28.9 + - - +
703B MET* 4.6 3.5 - - - +
160F GLU* 6.2 0.2 - - - -
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Residues in contact with VAL 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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147B LEU* 3.6 32.1 - - + +
150B LEU* 4.2 26.9 - - + -
151B VAL* 4.3 11.9 - - + -
156B LYS* 4.7 3.8 - - + -
157B SER 3.1 14.8 + - - +
158B PRO* 3.2 8.9 + - + +
160B GLU* 1.3 74.8 - - - +
162B PHE* 1.3 65.7 + - - +
164B ALA* 3.2 7.2 + - - +
165B LEU* 3.0 27.6 + - + +
270B ILE* 4.5 9.9 - - + -
699B LEU* 4.3 9.9 - - + -
703B MET* 4.3 10.1 - - + -
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Residues in contact with PHE 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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158B PRO 2.9 17.2 + - - +
159B GLU* 3.7 5.4 - - - +
161B VAL* 1.3 77.6 - - - +
163B GLU* 1.3 63.4 + - + +
165B LEU* 3.4 6.9 + - + +
166B LYS* 3.1 50.0 + - + +
267B LEU* 3.6 34.3 - - + -
270B ILE* 5.9 0.2 - - - +
272B ILE* 4.2 23.6 - - + -
274B GLU* 3.3 41.1 - - + -
275B ARG 3.9 7.9 - - - -
276B LEU* 4.1 18.8 - - + -
277B PRO* 4.0 12.3 - - + -
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Residues in contact with GLU 163 (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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159B GLU 3.0 18.7 + - - +
160B GLU* 3.7 6.7 - - - +
161B VAL 3.2 0.2 - - - -
162B PHE* 1.3 76.5 - - + +
164B ALA* 1.3 64.3 + - - +
166B LYS* 3.2 29.8 + - + +
167B ASN* 2.6 41.7 + - - +
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Residues in contact with ALA 164 (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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160B GLU 2.9 18.0 + - - +
161B VAL 3.2 5.1 + - - +
163B GLU* 1.3 75.5 - - - +
165B LEU* 1.3 64.6 + - - +
167B ASN* 2.9 17.1 + - - +
168B GLN* 3.2 12.6 + - - +
666B GLY* 5.8 0.7 - - - -
699B LEU* 3.7 19.3 - - + -
703B MET* 3.9 16.2 - - + -
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Residues in contact with LEU 165 (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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143B ILE* 5.2 8.7 - - + -
147B LEU* 4.6 11.7 - - + -
161B VAL* 3.0 28.1 + - + +
162B PHE* 3.7 8.1 - - - +
164B ALA* 1.3 75.1 - - - +
166B LYS* 1.3 62.6 + - - +
168B GLN* 3.1 20.4 + - - +
263B VAL* 4.2 21.5 - - + -
267B LEU* 5.2 9.0 - - + -
276B LEU* 4.3 12.3 - - + -
280B VAL* 4.1 2.4 - - - +
282B LEU* 3.5 42.6 - - + +
695B THR* 5.3 2.7 - - - +
699B LEU* 3.9 33.6 - - + +
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Residues in contact with LYS 166 (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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162B PHE* 3.1 52.4 + - + +
163B GLU* 3.2 28.7 + - + +
165B LEU* 1.3 74.8 - - - +
167B ASN* 1.3 63.0 + - - +
168B GLN 3.8 1.0 + - - +
274B GLU* 4.6 4.6 + - - -
276B LEU* 4.2 15.3 - - + -
277B PRO* 4.1 21.1 - - + +
280B VAL* 4.1 25.2 - - + +
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Residues in contact with ASN 167 (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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163B GLU* 2.6 31.4 + - - +
164B ALA* 2.9 11.6 + - - +
166B LYS* 1.3 82.0 + - - +
168B GLN* 1.3 59.3 + - - +
169B THR* 4.1 2.9 + - - -
634B LYS* 4.7 11.8 + - - +
665B ASN 5.1 0.3 - - - +
666B GLY* 3.7 12.4 - - - +
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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