Contacts of the strand formed by residues 168 - 172 (chain C) in PDB entry 1EJI
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 GLU 168 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A HIS* 4.1 7.6 - - - +
137A ARG* 3.3 32.0 + - - +
168A GLU* 3.5 33.0 - - + +
135C HIS* 3.2 45.2 + - - +
136C GLY 2.9 9.4 + - - +
137C ARG* 3.1 16.3 - - + +
138C ILE 2.9 24.7 + - - -
159C LYS* 3.6 22.3 + - - -
165C ILE 5.4 0.3 - - - +
167C PHE* 1.3 77.0 - - - +
169C SER* 1.3 59.3 + - - +
193C PHE* 3.7 5.6 - - + -
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Residues in contact with SER 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 2.8 31.1 + - - +
192A LEU 4.9 0.3 - - - +
138C ILE* 3.3 16.8 - - - -
151C HIS 4.8 3.4 - - - -
152C GLY* 3.9 20.7 - - - -
153C PHE 4.2 1.7 + - - -
154C MSE 2.7 36.0 - - - +
163C THR* 5.1 3.8 - - - -
164C SER* 3.3 16.2 - - - -
167C PHE 3.7 1.4 + - - -
168C GLU* 1.3 75.2 - - - +
170C MSE 1.3 61.3 + - - +
171C PRO* 4.7 1.5 - - - +
193C PHE* 4.1 1.3 - - - -
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Residues in contact with MSE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ARG* 4.8 1.3 - - - +
170A MSE 3.8 26.7 - - - +
189A ASN* 5.4 1.1 - - - +
192A LEU* 3.5 25.6 - - + +
193A PHE* 4.3 11.0 - - - +
138C ILE 3.1 4.4 + - - -
139C MSE 3.1 60.3 - - + +
140C GLY 3.6 1.3 + - - -
169C SER* 1.3 79.1 - - - +
171C PRO* 1.3 71.0 - - + +
189C ASN* 3.6 26.7 - - + +
193C PHE* 3.6 38.1 - - + -
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Residues in contact with PRO 171 (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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192A LEU* 3.4 47.2 - - + +
194A HIS* 5.5 4.9 - - + -
139C MSE 4.0 6.3 - - - +
140C GLY 3.0 15.5 - - - +
141C LEU 4.4 0.2 - - - -
142C ASP* 3.6 39.3 - - + +
151C HIS 6.1 0.4 - - - +
152C GLY 6.0 1.3 - - - +
154C MSE 6.6 0.4 - - + -
169C SER* 4.7 1.3 - - - +
170C MSE 1.3 93.2 - - + +
172C TYR* 1.3 61.1 + - - +
189C ASN* 5.0 0.7 + - - -
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Residues in contact with TYR 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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192A LEU* 5.8 0.2 - - - -
139C MSE 4.1 10.8 - - + -
140C GLY* 3.0 32.9 + - - -
141C LEU* 3.5 35.2 + - + +
142C ASP* 3.2 21.3 + - - +
171C PRO* 1.3 75.0 - - - +
173C LYS* 1.3 69.7 + - - +
181C ILE* 4.1 28.8 - - + +
182C ASN 5.7 0.9 - - - +
185C GLN* 4.9 4.0 - - - +
186C LEU* 3.7 54.1 - - + +
189C ASN* 5.7 2.5 - - - +
198C ILE* 4.5 4.7 - - + -
199C ILE 2.6 27.5 + - - -
200C ALA* 4.1 5.9 - - - -
201C GLY 4.9 1.4 + - - -
209C LEU* 5.8 0.9 - - - +
214C LEU* 4.5 8.0 - - + +
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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