Contacts of the helix formed by residues 157 - 167 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151H VAL* 4.8 0.7 - - - -
155H GLY 4.0 0.8 + - - -
156H LYS* 1.3 78.4 - - - +
158H PRO* 1.3 73.9 - - - +
159H GLU* 3.0 22.0 + - - +
160H GLU* 2.9 37.9 + - - +
161H VAL* 3.2 11.8 + - - +
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Residues in contact with PRO 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151H VAL* 3.9 23.8 - - + -
156H LYS 3.9 0.2 - - - -
157H SER* 1.3 86.3 - - - +
159H GLU* 1.3 64.1 + - - +
161H VAL* 3.3 10.2 + - + +
162H PHE* 2.9 30.3 + - - +
270H ILE* 3.4 34.0 - - + +
271H GLY* 5.3 0.9 - - - -
272H ILE* 3.8 22.7 - - + +
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Residues in contact with GLU 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H SER* 3.0 21.0 + - - +
158H PRO* 1.3 85.7 - - - +
160H GLU* 1.3 59.8 + - + +
162H PHE* 3.6 5.2 - - - +
163H GLU* 2.9 28.9 + - - +
272H ILE* 4.3 17.9 - - + +
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Residues in contact with GLU 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LYS* 4.0 26.2 - - + +
157H SER* 2.9 34.7 + - - +
159H GLU* 1.3 74.6 - - + +
161H VAL* 1.3 61.6 + - - +
163H GLU* 3.2 7.5 + - - +
164H ALA* 2.8 29.8 + - - +
703H MET* 4.5 6.0 - - - +
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Residues in contact with VAL 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H LEU* 3.6 31.9 - - + -
150H LEU* 4.2 24.5 - - + -
151H VAL* 4.5 8.3 - - + -
156H LYS* 4.5 8.3 - - + -
157H SER 3.2 15.6 + - - +
158H PRO* 3.6 9.6 - - + +
160H GLU* 1.3 73.4 - - - +
162H PHE* 1.3 65.1 + - - +
164H ALA* 3.1 3.5 + - - +
165H LEU* 3.0 29.2 + - + +
267H LEU* 5.1 0.2 - - + -
270H ILE* 4.5 11.0 - - + -
699H LEU* 4.4 7.9 - - + -
703H MET* 4.3 14.4 - - + -
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Residues in contact with PHE 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H PRO 2.9 18.3 + - - +
159H GLU* 3.6 6.1 - - - +
161H VAL* 1.3 77.6 - - - +
163H GLU* 1.3 62.8 + - - +
165H LEU* 3.4 3.4 + - - +
166H LYS* 3.1 50.5 + - + +
267H LEU* 3.7 39.6 - - + +
272H ILE* 4.0 26.2 - - + -
274H GLU* 3.1 40.6 - - + -
275H ARG 4.0 1.6 - - - -
276H LEU* 4.1 19.7 - - + -
277H PRO* 4.0 18.2 - - + -
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Residues in contact with GLU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H GLU 2.9 18.5 + - - +
160H GLU* 3.6 7.4 - - - +
161H VAL 3.2 0.2 - - - -
162H PHE* 1.3 73.9 - - - +
164H ALA* 1.3 67.5 + - - +
166H LYS* 3.4 27.2 + - - +
167H ASN* 3.1 47.5 + - - +
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Residues in contact with ALA 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H GLU 2.8 20.7 + - - +
161H VAL 3.1 4.7 + - - +
163H GLU* 1.3 74.1 - - - +
165H LEU* 1.3 63.1 + - - +
167H ASN* 3.0 16.2 + - - +
168H GLN* 3.1 13.0 + - - +
666H GLY* 5.7 0.7 - - - -
699H LEU* 3.6 20.4 - - + +
703H MET* 3.9 18.2 - - + -
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ILE* 5.2 3.1 - - + -
147H LEU* 4.7 7.0 - - + -
161H VAL* 3.0 16.1 + - + +
162H PHE* 3.7 6.7 - - - +
163H GLU 3.3 0.2 - - - -
164H ALA* 1.3 77.4 - - - +
166H LYS* 1.3 61.5 + - - +
168H GLN* 3.0 20.8 + - - +
263H VAL* 4.3 17.9 - - + -
267H LEU* 4.0 28.3 - - + -
276H LEU* 4.1 13.0 - - + +
280H VAL* 5.1 1.9 - - - +
282H LEU* 3.5 39.6 - - + +
695H THR* 4.4 12.3 - - + -
699H LEU* 3.8 33.4 - - + -
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Residues in contact with LYS 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H PHE* 3.1 48.1 + - + +
163H GLU* 3.7 27.8 + - - +
164H ALA 3.3 0.2 - - - -
165H LEU* 1.3 75.8 - - - +
167H ASN* 1.3 66.2 + - - +
168H GLN 3.4 2.3 + - - +
274H GLU* 4.9 2.4 + - - -
276H LEU* 4.1 15.0 - - + -
277H PRO* 4.2 21.6 - - + +
280H VAL* 4.2 25.4 - - + +
281H SER 5.8 0.2 + - - -
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Residues in contact with ASN 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H GLU* 3.1 35.7 + - - +
164H ALA* 3.0 12.3 + - - +
166H LYS* 1.3 81.4 + - - +
168H GLN* 1.3 60.5 + - - +
169H THR* 4.7 2.3 + - - -
634H LYS* 4.7 11.7 + - - +
666H GLY* 3.6 13.2 - - - +
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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