Contacts of the strand formed by residues 114 - 119 (chain F) in PDB entry 3EI4
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 ALA 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F PHE* 4.4 5.5 - - + -
113F ARG* 1.3 71.8 - - - +
115F THR* 1.3 57.9 + - - +
116F SER 5.2 0.7 - - - +
129F VAL* 4.5 12.6 - - + -
130F GLY 3.5 9.0 - - - +
338F THR* 2.6 30.3 + - - +
396F SER* 5.6 0.3 - - - -
397F LEU* 5.4 0.2 - - - -
410F ALA* 3.9 29.6 - - + +
412F GLY* 2.8 21.1 + - - +
413F TYR* 4.5 4.3 - - - +
414F HIS 4.7 5.6 - - - +
415F ILE* 5.1 2.9 - - + -
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ARG* 4.2 2.7 - - - +
114F ALA* 1.3 80.3 - - - +
116F SER* 1.3 64.1 + - - +
130F GLY 2.9 3.4 + - - -
131F SER* 3.1 21.3 + - - -
132F LYS* 3.5 37.5 - - + +
158F SER* 3.8 6.7 + - - +
159F ILE 2.7 23.9 + - - +
160F THR* 4.8 5.5 - - - +
338F THR* 3.8 23.2 - - + +
397F LEU* 3.7 14.2 - - - +
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Residues in contact with SER 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ALA* 5.2 0.6 - - - +
115F THR* 1.3 78.9 + - - +
117F LEU* 1.3 60.1 + - - +
129F VAL* 3.3 7.3 - - - +
130F GLY* 2.6 30.9 + - - -
159F ILE* 2.6 36.4 + - - -
160F THR 3.4 1.7 - - - -
161F GLY* 3.2 15.6 + - - -
162F LEU* 3.4 27.0 - - - +
397F LEU* 4.0 5.3 - - - +
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Residues in contact with LEU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F SER* 1.3 74.9 - - - +
118F ALA* 1.3 81.6 + - - +
119F TRP* 4.7 5.4 - - + +
127F VAL* 4.3 11.7 - - + -
128F ALA 3.7 10.1 - - - +
129F VAL* 4.5 9.0 - - + -
162F LEU* 4.0 6.5 + - - +
163F LYS* 5.9 1.9 - - - -
397F LEU* 4.0 24.3 - - + +
399F GLU* 4.2 25.5 - - + +
408F ALA* 3.6 45.5 - - + +
409F SER 4.6 0.4 - - - -
410F ALA* 4.1 19.5 - - + +
415F ILE* 6.2 1.6 - - + -
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 1.3 77.5 - - - +
119F TRP* 1.3 60.5 + - - +
127F VAL* 3.5 2.8 - - - -
128F ALA* 2.7 39.1 + - + +
162F LEU* 3.2 37.2 - - + +
163F LYS* 4.4 5.2 - - + -
164F PHE* 3.6 21.0 - - + +
399F GLU* 6.3 0.7 - - - -
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Residues in contact with TRP 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 4.8 1.6 - - + -
118F ALA* 1.3 75.1 - - - +
120F HIS* 1.3 68.4 + - - +
121F PRO* 3.1 5.4 - - - +
123F HIS 4.5 1.3 - - - -
124F PRO 3.8 17.5 - - - -
125F SER 4.1 0.4 - - - -
126F THR 3.2 23.8 - - - -
127F VAL* 3.4 15.7 - - + -
141F PHE* 3.6 30.5 - + - -
164F PHE* 3.5 9.9 - - - -
399F GLU* 3.1 39.9 + - + +
400F PHE 2.9 21.7 + - - +
401F ASN* 2.8 34.5 - - - -
402F PRO* 4.1 14.8 - - + -
406F THR* 4.1 5.4 - - + -
407F LEU 4.6 0.2 - - - -
408F ALA* 3.6 28.9 - - + +
417F ILE* 5.0 0.4 - - + -
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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