Contacts of the strand formed by residues 169 - 174 (chain C) in PDB entry 1EAK
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 ILE 169 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C TRP* 4.2 6.5 - - + +
124C ILE* 4.2 17.3 - - + -
125C THR 3.0 8.4 + - - +
126C TYR* 3.2 5.0 - - + +
127C ARG 3.1 23.4 + - - +
148C PHE* 3.8 30.3 - - + -
159C PHE* 4.8 0.2 - - + -
167C ALA* 4.5 0.7 - - - -
168C ASP* 1.3 81.4 - - - +
170C MET* 1.3 61.3 + - - +
171C ILE* 4.1 15.0 - - + -
203C GLY* 3.3 27.8 - - - +
205C SER* 3.8 12.6 - - - +
405C PHE* 4.5 0.7 - - + +
408C ALA* 3.5 23.8 - - + +
409C MET* 4.3 11.4 - - - -
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Residues in contact with MET 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ARG* 3.6 19.3 - - - +
129C ILE* 3.1 46.7 - - + -
165C GLY 4.2 5.4 - - - +
166C GLU* 4.3 20.4 - - - +
167C ALA* 3.5 41.3 - - - +
169C ILE* 1.3 73.4 - - - +
171C ILE* 1.3 61.1 + - - +
172C ASN 3.9 0.5 + - - -
204C ASP* 3.3 32.3 + - - +
205C SER 3.1 22.2 + - - +
206C HIS* 4.4 4.1 - - - +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C TYR* 3.6 30.5 - - + -
127C ARG 2.9 14.7 + - - +
128C ILE* 3.6 5.6 - - + -
129C ILE* 2.9 28.3 + - - +
130C GLY 3.6 3.1 + - - +
144C PHE* 3.4 46.2 - - + -
148C PHE* 3.7 4.7 - - + -
169C ILE* 4.1 13.5 - - + +
170C MET* 1.3 72.6 - - - +
172C ASN* 1.3 66.0 + - - +
173C PHE* 5.2 0.7 - - + -
205C SER* 3.3 4.5 - - - +
207C PHE* 3.9 14.4 - - + -
405C PHE* 3.5 29.8 - - + -
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Residues in contact with ASN 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE* 3.3 34.1 - - + +
130C GLY* 3.4 18.9 - - - +
170C MET 3.9 0.6 + - - -
171C ILE* 1.3 75.8 - - - +
173C PHE* 1.3 93.1 + - - +
205C SER 3.2 6.9 + - - +
206C HIS* 3.1 22.4 - - + +
207C PHE* 2.9 23.8 + - - -
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLY 3.3 24.9 - - - -
131C TYR* 3.4 26.9 - - - +
132C THR* 3.6 28.5 - - + -
140C VAL* 4.4 2.0 - - + -
144C PHE* 3.7 18.6 - + - -
171C ILE* 5.2 0.9 - - + -
172C ASN* 1.3 97.6 + - - +
174C GLY* 1.3 58.9 + - - +
207C PHE* 3.2 26.7 - - + +
209C ASP* 4.0 16.1 - - + +
213C TRP* 3.8 24.7 - + - -
397C LEU* 3.6 29.2 - - + -
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Residues in contact with GLY 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLN* 3.6 10.8 - - - -
172C ASN 4.2 0.6 + - - -
173C PHE* 1.3 74.2 - - - +
175C ARG* 1.3 55.7 + - - -
178C HIS* 3.9 18.0 - - - -
184C PHE* 3.0 15.6 - - - -
207C PHE 2.7 11.4 + - - +
209C ASP* 2.8 27.1 + - - +
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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
------------------------------------------------------------
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