Contacts of the strand formed by residues 168 - 172 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A HIS* 3.2 45.8 + - - +
136A GLY 2.9 9.6 + - - +
137A ARG* 3.1 15.8 - - + +
138A ILE* 2.9 24.5 + - - -
159A LYS* 4.7 14.4 + - - -
165A ILE 5.6 0.9 - - - +
167A PHE* 1.3 77.6 - - - +
169A SER* 1.3 58.5 + - - +
193A PHE* 3.7 5.8 - - + -
135C HIS* 4.2 11.3 - - - +
137C ARG* 3.3 27.7 + - - +
168C GLU* 3.5 31.9 - - + +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 3.3 15.5 - - - -
140A GLY 6.1 0.4 - - - -
151A HIS 4.9 0.9 - - - -
152A GLY* 3.5 31.6 + - - -
154A MSE 3.9 13.6 - - - +
163A THR* 5.2 2.0 - - - -
164A SER* 3.5 26.6 + - - +
167A PHE* 3.7 2.4 + - - -
168A GLU* 1.3 76.7 - - - +
170A MSE 1.3 61.5 + - - +
171A PRO* 4.8 0.6 - - - +
193A PHE* 4.1 0.7 - - - -
137C ARG* 2.7 32.3 + - - +
192C LEU 5.2 0.2 - - - +
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Residues in contact with MSE 170 (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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138A ILE 3.2 4.2 + - - -
139A MSE 3.2 59.5 - - + +
140A GLY 4.5 1.1 - - - -
152A GLY 5.7 1.1 - - - -
169A SER* 1.3 78.5 - - - +
171A PRO* 1.3 78.1 - - + +
189A ASN* 3.5 26.7 - - + +
193A PHE* 3.7 39.7 - - + -
137C ARG* 4.7 1.8 - - - +
170C MSE 3.8 25.8 - - - +
189C ASN* 6.1 0.7 - - - +
192C LEU* 3.6 19.7 - - + +
193C PHE* 4.2 11.7 - - - -
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Residues in contact with PRO 171 (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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139A MSE 4.1 5.7 - - - +
140A GLY 3.1 14.4 - - - +
141A LEU 4.5 0.2 - - - -
142A ASP* 3.6 41.1 - - + +
152A GLY 5.2 8.9 - - - +
154A MSE 5.9 5.2 - - + -
169A SER* 4.8 1.3 - - - +
170A MSE 1.3 100.0 - - + +
172A TYR* 1.3 60.3 + - - +
189A ASN* 5.1 1.2 + - - -
192C LEU* 3.6 40.5 - - + +
194C HIS* 5.7 3.4 - - + -
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Residues in contact with TYR 172 (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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139A MSE 4.1 11.2 - - + -
140A GLY* 2.9 34.3 + - - -
141A LEU* 3.5 35.9 + - + +
142A ASP 3.2 21.0 + - - -
171A PRO* 1.3 74.7 - - - +
173A LYS* 1.3 69.4 + - - +
181A ILE* 4.2 29.8 - - + +
182A ASN 5.6 1.1 - - - +
185A GLN* 4.9 4.3 - - - +
186A LEU* 3.7 54.5 - - + +
189A ASN* 5.8 2.2 - - - +
198A ILE* 4.4 4.7 - - + -
199A ILE 2.5 27.5 + - - -
200A ALA* 4.1 6.4 - - - -
201A GLY 4.9 1.2 + - - -
209A LEU* 5.8 0.7 - - - +
214A LEU* 4.5 8.7 - - + +
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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