Contacts of the strand formed by residues 117 - 122 (chain P) in PDB entry 1E33
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 117 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A NAG 3.4 24.2 - - + +
115P GLY 3.9 1.4 + - - -
116P TYR* 1.3 72.5 - - - +
118P THR* 1.3 58.2 + - - +
119P GLY 4.0 0.3 + - - -
142P HIS* 3.6 19.3 - - + +
143P ARG* 4.0 14.4 - - - +
208P LEU* 3.5 40.1 - - + +
211P ASP* 4.2 2.5 - - + -
212P ALA* 3.6 23.1 - - + +
215P GLU* 4.7 6.1 - - - +
217P ARG* 3.7 29.7 - - - +
218P PRO 2.9 12.1 + - - +
219P PHE* 3.4 5.0 - - - +
220P PHE 3.1 21.1 + - - +
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Residues in contact with THR 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P ALA* 4.1 20.6 - - - +
111P LEU* 4.5 1.1 - - + -
112P ALA* 4.3 5.2 - - - +
116P TYR* 3.9 16.4 - - + +
117P LEU* 1.3 74.6 - - - +
119P GLY* 1.4 60.6 - - - +
140P GLY 2.9 22.0 + - - +
141P PHE* 3.2 6.1 - - - -
142P HIS* 2.8 43.7 + - - +
143P ARG* 3.1 7.1 + - - +
208P LEU* 4.2 3.5 - - - +
220P PHE* 3.6 31.0 - - + -
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Residues in contact with GLY 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P THR* 1.4 77.0 - - - +
120P MET* 1.3 59.5 + - - -
141P PHE* 3.6 6.0 - - - -
143P ARG* 3.3 10.1 - - - -
204P PHE* 4.4 1.6 - - - -
208P LEU* 3.9 20.0 - - - +
220P PHE 2.9 13.6 + - - +
221P LEU* 3.3 10.6 - - - +
222P TYR* 2.8 27.5 + - - +
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Residues in contact with MET 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P GLY* 1.3 74.5 - - - -
121P ALA* 1.3 65.5 + - - +
122P GLY 3.5 19.5 - - - +
123P LYS 3.2 30.5 - - - +
124P TRP* 3.7 30.5 - - + -
136P PRO* 4.1 12.1 - - - -
141P PHE* 3.7 21.1 - - + -
143P ARG 2.8 10.7 + - - +
144P PHE* 3.2 17.5 - - + -
145P LEU 3.2 21.1 + - - -
204P PHE* 3.5 6.6 - - - -
222P TYR* 3.2 31.9 - - + +
224P ALA* 4.5 1.8 - - + -
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Residues in contact with ALA 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P MET* 1.3 79.5 - - - +
122P GLY* 1.3 57.5 + - - +
145P LEU 3.2 10.1 - - - +
201P TYR* 4.2 20.2 - - + +
204P PHE* 3.9 21.7 - - + -
205P ALA* 6.0 1.1 - - + -
221P LEU* 4.6 3.8 - - + +
222P TYR 2.7 7.7 + - - +
223P TYR* 3.6 18.8 - - + -
224P ALA 3.0 25.1 + - - +
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Residues in contact with GLY 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P MET* 3.5 9.8 - - - +
121P ALA* 1.3 72.9 - - - +
123P LYS* 1.4 63.8 + - - -
144P PHE* 3.7 1.2 - - - -
145P LEU 3.1 12.1 + - - -
146P GLY* 3.5 3.5 - - - -
147P ILE 3.0 21.5 + - - +
201P TYR* 3.7 23.5 - - - -
224P ALA 3.4 7.6 - - - -
226P HIS* 3.9 4.7 - - - -
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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