Contacts of the helix formed by residues 203 - 208 (chain B) in PDB entry 1EKV
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 LEU 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PRO* 4.9 4.0 - - + -
71B SER 5.9 0.4 - - - +
73B GLN 3.9 8.1 - - - +
74B LEU* 4.0 2.7 - - + -
75B PHE* 4.1 3.4 - - - -
103B SER* 3.7 30.5 - - - +
106B ARG* 5.0 0.9 - - + -
107B LEU* 3.9 39.3 - - + -
198B VAL* 3.0 42.4 - - + +
201B TYR* 3.2 19.8 + - + +
202B LYS* 1.3 76.0 - - - +
204B GLY* 1.3 66.3 + - - +
205B GLY* 4.2 6.7 - - - +
206B ASN* 2.9 19.0 + - - +
207B TYR* 3.2 12.2 - - - -
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Residues in contact with GLY 204 (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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69A HIS 2.9 27.7 + - - -
70A TYR* 3.3 16.3 - - - +
71A SER* 3.5 6.3 - - - -
73B GLN* 3.5 24.5 + - - -
75B PHE* 4.0 6.7 - - - -
203B LEU* 1.3 70.9 - - - +
205B GLY* 1.3 61.5 + - - +
207B TYR* 2.9 14.3 + - - -
208B GLY 3.5 0.2 + - - -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.4 19.3 - - - -
205A GLY* 4.3 15.3 - - - -
71B SER* 3.5 12.2 + - - -
203B LEU* 3.1 6.2 + - - +
204B GLY* 1.3 75.7 - - - +
206B ASN* 1.3 64.6 + - - +
209B PRO* 3.3 21.2 - - - +
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Residues in contact with ASN 206 (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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194A TRP* 6.0 3.0 - - - -
192B ARG* 3.3 42.5 + - + +
193B ALA* 5.6 0.6 - - - +
198B VAL* 3.2 37.8 + - - +
199B GLY* 3.4 13.7 - - - +
201B TYR 2.8 26.7 - - - +
203B LEU* 2.9 16.6 + - - +
205B GLY* 1.3 78.0 - - - +
207B TYR* 1.3 61.1 + - + +
209B PRO* 3.8 6.2 - - - +
210B THR* 3.7 13.7 - - - +
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Residues in contact with TYR 207 (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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70A TYR* 3.9 24.5 - + + -
155A VAL* 4.5 8.5 - - + -
75B PHE* 3.8 18.6 - + - -
192B ARG* 3.2 26.0 + - - -
202B LYS* 4.0 7.6 + - - +
203B LEU 3.2 26.2 - - - -
204B GLY 2.9 8.1 + - - +
206B ASN* 1.3 77.5 - - + +
208B GLY* 1.3 67.3 + - - +
209B PRO* 3.2 3.8 - - - -
210B THR* 2.6 35.8 + - + +
211B VAL* 3.8 2.3 + - - +
240B THR* 3.6 13.9 - - + -
266B LEU* 4.6 5.7 - - - +
370B PLP 2.6 28.9 + - + +
371B TRS 3.0 33.0 + - - -
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Residues in contact with GLY 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 2.8 31.0 + - - -
71A SER* 4.4 5.8 - - - -
72A LEU* 4.1 13.1 - - - +
107A LEU* 3.7 15.9 - - - +
204B GLY 3.5 2.2 + - - -
207B TYR* 1.3 73.4 - - - +
209B PRO* 1.3 63.4 - - - +
210B THR 3.2 3.3 + - - -
211B VAL* 3.4 20.1 + - - +
212B LEU 4.9 0.3 + - - -
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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