Contacts of the helix formed by residues 141 - 151 (chain H) in PDB entry 3KDO
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 PHE 141 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140H ALA* 1.3 94.0 - - + +
142H GLY* 1.3 65.4 + - - +
144H GLU* 4.1 2.3 + - - +
145H GLY* 2.8 49.0 + - - -
146H VAL* 4.5 1.6 - - + +
149H MET* 5.4 11.7 - - + -
250H LYS 5.6 0.7 - - - -
272H ALA* 5.9 1.8 - - - -
275H GLY* 3.5 27.4 - - - -
276H LEU 3.8 7.0 - - - -
277H ALA* 3.7 39.5 - - + -
311H ASP* 2.8 14.5 + - - +
360H LYS* 4.0 14.6 + - - +
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Residues in contact with GLY 142 (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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139H PRO* 3.5 14.9 - - - +
141H PHE* 1.3 77.9 - - - +
143H ILE* 1.3 64.0 + - - -
146H VAL* 3.2 22.2 + - - +
311H ASP* 2.9 25.5 + - - -
360H LYS* 4.5 4.9 - - - -
361H ALA 3.0 16.2 - - - -
363H PHE* 4.9 0.2 - - - -
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Residues in contact with ILE 143 (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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142H GLY* 1.3 70.5 - - - -
144H GLU* 1.3 66.1 + - - +
146H VAL* 3.0 4.9 + - - +
147H ARG* 3.0 35.7 + - + +
338H ARG* 3.5 38.8 - - + -
361H ALA* 2.9 24.4 + - + +
362H ALA 3.5 21.5 - - - +
363H PHE* 3.7 32.9 - - + +
364H PRO* 4.4 3.1 - - + -
385H ASP* 4.4 18.2 - - + +
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Residues in contact with GLU 144 (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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141H PHE 4.1 2.7 + - - +
142H GLY 3.4 0.2 - - - -
143H ILE* 1.3 81.4 - - - +
145H GLY* 1.3 63.3 + - - +
147H ARG* 3.4 5.1 + - - +
148H LYS* 3.2 24.7 + - - +
360H LYS* 6.0 4.7 - - + +
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Residues in contact with GLY 145 (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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141H PHE* 2.8 50.0 + - - -
142H GLY 3.9 0.2 - - - -
144H GLU* 1.3 74.3 - - - +
146H VAL* 1.3 56.5 + - - +
148H LYS* 4.0 4.8 - - - +
149H MET* 3.2 25.8 + - - +
360H LYS* 6.2 0.4 - - - -
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Residues in contact with VAL 146 (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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141H PHE* 4.5 10.3 - - + -
142H GLY 3.2 14.1 + - - +
143H ILE 3.0 6.9 + - - +
145H GLY* 1.3 74.3 - - - +
147H ARG* 1.3 61.4 + - - +
148H LYS 3.2 1.8 - - - -
149H MET* 3.2 6.4 + - - +
150H LEU* 2.8 51.2 + - + +
157H ILE* 4.9 4.5 - - + -
251H HIS* 4.4 9.4 - - + +
277H ALA* 4.6 5.2 - - + -
311H ASP* 5.0 2.2 - - + -
312H GLN* 3.4 33.2 - - + +
363H PHE* 3.9 22.2 - - + -
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Residues in contact with ARG 147 (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* 3.0 23.2 + - + +
144H GLU* 4.0 5.4 - - - +
146H VAL* 1.3 76.5 - - - +
148H LYS* 1.3 53.4 + - - +
150H LEU* 5.1 1.3 - - - -
151H GLU* 2.6 28.8 + - - -
152H ILE* 2.8 59.1 + - - +
153H LYS* 3.1 22.4 + - - +
154H ASP 3.1 8.4 + - - -
155H ARG 2.7 22.6 + - - -
156H PRO* 4.1 2.0 - - - +
157H ILE* 4.0 6.2 - - + +
363H PHE* 4.0 21.5 - - + -
384H THR 3.1 20.6 + - - -
385H ASP* 2.9 33.7 + - - +
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Residues in contact with LYS 148 (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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144H GLU 3.2 17.2 + - - +
145H GLY* 4.0 5.8 - - - +
147H ARG* 1.3 74.2 - - - +
149H MET* 1.3 67.6 + - - +
151H GLU* 3.0 20.7 + - - +
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Residues in contact with MET 149 (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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141H PHE* 5.4 11.2 - - + -
145H GLY 3.2 16.1 + - - +
146H VAL* 3.2 7.1 + - - +
148H LYS* 1.3 81.7 - - - +
150H LEU* 1.3 67.1 + - + +
151H GLU* 3.3 1.7 + - - +
223H LYS* 3.5 19.8 - - - +
225H THR* 3.4 11.2 - - - +
250H LYS* 2.8 61.0 + - + +
251H HIS* 3.2 34.3 - - + +
277H ALA* 5.0 6.3 - - - -
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Residues in contact with LEU 150 (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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146H VAL* 2.8 34.6 + - + +
147H ARG* 5.1 0.4 - - - -
149H MET* 1.3 85.1 - - + +
151H GLU* 1.3 71.7 + - - +
152H ILE* 3.4 23.3 + - + +
157H ILE* 3.8 30.3 - - + -
186H ASP* 4.8 4.7 - - + +
187H TYR* 5.6 0.4 - - + -
223H LYS* 3.4 26.4 + - + +
224H LYS* 4.2 12.3 - - - +
225H THR* 3.6 39.7 - - + -
227H PHE* 5.9 1.6 - - + -
250H LYS* 4.9 0.7 - - - +
251H HIS* 5.0 1.8 - - + -
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Residues in contact with GLU 151 (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 ARG 2.6 17.6 + - - -
148H LYS* 3.0 19.1 + - - +
149H MET 3.8 3.6 - - - +
150H LEU* 1.3 79.5 - - - +
152H ILE* 1.3 58.3 + - - +
153H LYS 4.1 1.3 + - - -
221H GLY 5.2 4.7 - - - +
223H LYS* 2.9 35.0 - - + +
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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