Contacts of the helix formed by residues 157 - 167 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D VAL* 4.1 0.9 - - - -
155D GLY 3.9 1.2 + - - -
156D LYS* 1.3 77.0 - - - +
158D PRO* 1.3 73.9 - - - +
159D GLU* 2.9 32.0 + - - +
160D GLU* 3.0 31.2 + - - +
161D VAL* 3.2 12.1 + - - +
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Residues in contact with PRO 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 3.9 20.4 - - + -
156D LYS 4.3 0.2 - - - +
157D SER* 1.3 88.2 - - - +
159D GLU* 1.3 56.9 + - + +
161D VAL* 3.2 5.8 + - + +
162D PHE* 2.9 30.1 + - - +
270D ILE* 3.5 31.3 - - + +
271D GLY* 5.3 1.1 - - - -
272D ILE* 3.9 22.3 - - + +
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Residues in contact with GLU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D SER* 2.9 28.0 + - - +
158D PRO* 1.3 79.7 - - + +
160D GLU* 1.3 62.7 + - - +
162D PHE* 3.4 8.0 + - - +
163D GLU* 2.9 31.2 + - - +
272D ILE* 4.1 7.5 - - + +
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLY 5.2 0.7 - - - +
156D LYS* 3.6 36.8 + - + +
157D SER* 3.0 40.2 + - - +
159D GLU* 1.3 84.2 - - - +
161D VAL* 1.3 56.5 + - - +
163D GLU* 3.5 6.4 + - - +
164D ALA* 3.0 27.0 + - - +
703D MET* 4.3 7.3 - - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.5 31.2 - - + +
150D LEU* 4.2 24.2 - - + -
151D VAL* 4.3 12.6 - - + -
156D LYS* 4.5 4.3 - - + -
157D SER 3.2 13.1 + - - +
158D PRO* 3.2 7.2 + - + +
160D GLU* 1.3 75.0 - - - +
162D PHE* 1.3 65.4 + - - +
164D ALA* 3.1 3.3 + - - +
165D LEU* 3.0 28.6 + - + +
267D LEU* 5.0 0.7 - - + -
270D ILE* 4.6 10.5 - - + -
699D LEU* 4.1 11.2 - - + +
703D MET* 4.2 16.4 - - + -
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D PRO 2.9 17.8 + - - +
159D GLU* 3.7 6.1 - - - +
161D VAL* 1.3 76.0 - - - +
163D GLU* 1.3 63.2 + - - +
165D LEU* 3.2 5.8 + - + +
166D LYS* 3.0 52.0 + - + +
267D LEU* 3.7 39.4 - - + +
272D ILE* 4.1 23.3 - - + -
274D GLU* 3.2 41.5 - - + -
275D ARG 3.9 2.0 - - - -
276D LEU* 4.1 17.5 - - + -
277D PRO* 3.9 18.6 - - + -
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Residues in contact with GLU 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLU 2.9 19.4 + - - +
160D GLU* 3.8 6.7 - - - +
162D PHE* 1.3 77.5 - - - +
164D ALA* 1.3 62.8 + - - +
166D LYS* 3.3 26.9 + - - +
167D ASN* 3.0 46.2 + - - +
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Residues in contact with ALA 164 (chain D).
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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160D GLU 3.0 16.5 + - - +
161D VAL 3.1 5.1 + - - +
163D GLU* 1.3 76.1 - - - +
165D LEU* 1.3 63.6 + - - +
167D ASN* 3.1 16.1 + - - +
168D GLN* 3.2 14.2 + - - +
666D GLY* 5.6 1.2 - - - -
699D LEU* 3.7 19.0 - - + +
703D MET* 3.9 16.8 - - + -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D ILE* 5.4 3.6 - - + -
147D LEU* 4.8 5.2 - - + -
161D VAL* 3.0 18.1 + - + +
162D PHE* 3.2 7.6 + - - +
164D ALA* 1.3 76.1 - - - +
166D LYS* 1.3 60.8 + - - +
168D GLN* 3.1 14.5 + - - +
263D VAL* 4.1 18.6 - - + -
267D LEU* 3.8 30.3 - - + -
276D LEU* 4.0 11.9 - - + -
280D VAL* 3.9 3.5 - - - +
282D LEU* 3.4 44.1 - - + +
695D THR* 4.4 11.9 - - + -
699D LEU* 3.8 33.4 - - + -
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D PHE* 3.0 43.3 + - + +
163D GLU* 3.3 27.9 + - - +
164D ALA 3.3 0.4 - - - -
165D LEU* 1.3 75.5 - - - +
167D ASN* 1.3 66.3 + - - +
168D GLN 4.9 0.5 - - - +
276D LEU* 4.1 8.1 - - + -
277D PRO* 3.5 37.5 - - + -
280D VAL* 4.0 26.4 - - + +
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Residues in contact with ASN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D GLU* 3.0 40.7 + - - +
164D ALA* 3.1 9.7 + - - +
166D LYS* 1.3 82.1 + - - +
168D GLN* 1.3 59.9 + - - +
169D THR* 4.8 1.8 + - - -
634D LYS* 6.1 1.0 - - - -
666D GLY* 3.6 14.5 - - - +
667D SER* 5.8 0.2 - - - -
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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