Contacts of the helix formed by residues 204 - 208 (chain A) in PDB entry 1EKF
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 GLY 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.3 27.6 + - - +
75A PHE* 4.2 3.4 - - - -
202A LYS 4.1 1.4 + - - -
203A LEU* 1.3 70.8 - - - +
205A GLY* 1.3 61.1 + - - +
207A TYR* 3.0 16.2 + - - -
69B HIS 3.2 25.4 - - - -
70B TYR* 3.2 17.2 - - - +
71B SER* 3.4 6.5 - - - -
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER* 3.7 9.6 + - - -
73A GLN 5.0 0.2 + - - -
203A LEU* 2.9 6.5 + - - +
204A GLY* 1.3 74.3 - - - +
206A ASN* 1.3 64.1 + - - +
207A TYR 3.2 0.2 - - - -
209A PRO* 3.2 22.0 - - - +
71B SER* 3.4 20.1 - - - -
205B GLY* 4.2 15.9 - - - -
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.7 28.3 + - - +
193A ALA* 5.7 0.2 - - - +
194A TRP* 6.4 0.2 - - - -
198A VAL* 3.1 37.1 + - - +
199A GLY* 3.9 11.4 - - - +
201A TYR 2.9 26.3 - - - +
203A LEU* 2.9 16.8 + - - +
205A GLY* 1.3 79.3 - - - +
207A TYR* 1.3 74.1 + - + +
209A PRO* 4.1 5.0 - - - +
210A THR* 3.5 18.0 - - - +
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Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 3.6 29.4 - + - -
192A ARG* 4.6 4.6 + - - -
201A TYR 4.7 1.6 + - - -
202A LYS* 3.5 15.2 - - - +
203A LEU 3.3 26.0 - - - -
204A GLY* 3.0 6.2 + - - +
206A ASN* 1.3 89.6 - - + +
208A GLY* 1.3 67.4 + - - +
209A PRO 3.2 2.7 - - - -
210A THR* 2.7 30.9 + - + -
211A VAL 3.8 1.9 + - - -
240A THR* 3.9 23.8 - - + -
266A LEU* 4.7 1.4 - - - +
370A PLP 2.5 41.7 + - + +
70B TYR* 3.7 25.6 - + + -
155B VAL* 4.2 17.0 - - + +
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Residues in contact with GLY 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLY 3.6 1.2 + - - -
207A TYR* 1.3 74.9 - - - +
209A PRO* 1.3 68.9 - - - +
210A THR 3.1 1.2 + - - -
211A VAL* 3.3 21.2 + - - +
212A LEU 4.9 0.3 + - - -
70B TYR* 2.8 28.0 + - - -
71B SER 4.3 5.8 - - - -
72B LEU* 4.0 13.6 - - - +
106B ARG* 4.8 0.5 + - - -
107B LEU* 3.8 14.4 - - - +
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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