Contacts of the strand formed by residues 139 - 145 (chain E) in PDB entry 1YKN
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 139 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ILE 3.9 0.3 - - - +
129E SER* 3.3 3.6 - - - -
130E LEU* 2.7 40.3 + - + +
135E ILE* 4.3 23.3 - - + -
137E ILE* 4.1 11.4 - - + +
138E HIS* 1.3 72.2 - - - +
140E HIS* 1.3 62.1 + - - +
141E THR* 5.5 0.7 - - - +
189E ILE* 4.3 19.3 - - + -
197E PHE* 3.6 49.1 - - + -
313F ARG* 6.3 1.1 - - - +
319F ALA* 5.8 2.9 - - + -
330F ARG 5.0 0.2 - - - +
332F PRO* 4.0 26.9 - - + -
336F LEU* 4.5 9.0 - - + -
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Residues in contact with HIS 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E ILE 3.3 7.7 + - - +
129E SER* 3.8 13.4 + - - -
138E HIS* 3.7 38.1 + + - -
139E LEU* 1.3 71.9 - - - +
141E THR* 1.3 61.3 + - - +
197E PHE* 3.3 7.9 - - - +
198E PHE* 2.9 49.7 + - + +
199E ASP* 5.1 1.3 - - - -
200E PHE* 3.2 46.7 + + + -
311F ARG* 4.0 14.6 + - - -
313F ARG* 4.4 13.6 + - - -
470F ILE* 4.1 14.9 - - + +
471F ALA* 5.4 0.2 - - - -
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ASN* 3.9 1.4 - - - +
128E ILE* 2.8 51.5 + - + +
130E LEU* 6.1 2.0 - - + -
139E LEU 5.6 1.1 - - - +
140E HIS* 1.3 77.1 - - - +
142E ARG* 1.3 73.3 + - - +
170E LEU* 3.4 13.0 - - - +
185E PHE* 4.4 18.1 - - + -
187E ILE* 4.4 9.6 - - + -
195E THR* 3.5 4.0 - - + +
196E VAL 2.9 22.1 + - - -
197E PHE* 3.9 12.3 - - + -
198E PHE* 3.9 8.7 - - - -
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Residues in contact with ARG 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E MET* 3.4 36.0 - - - +
125E HIS* 3.6 25.7 + - + -
126E ILE 3.2 7.0 - - - +
127E ASN* 3.6 18.2 + - - +
141E THR* 1.3 83.4 + - - +
143E LEU* 1.3 60.1 + - - +
144E TYR* 3.0 41.6 + - + -
155E CYS* 4.4 0.2 - - - -
157E VAL* 3.6 26.3 - - - +
170E LEU* 3.5 25.5 - - + +
185E PHE* 3.9 6.7 - - - -
198E PHE* 3.8 17.8 - - + -
339F ILE* 4.5 3.8 - - - +
342F SER* 3.7 2.8 + - - -
344F SER* 3.6 11.7 - - - -
345F GLU* 2.9 26.7 + - - -
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 4.2 26.0 - - + -
104E TRP* 4.5 5.8 - - + -
125E HIS* 3.1 7.4 - - - -
126E ILE* 2.7 48.2 + - + +
128E ILE* 3.8 21.7 - - + +
142E ARG* 1.3 73.2 - - - +
144E TYR* 1.3 69.6 + - - +
145E PHE* 3.8 29.6 - - + -
170E LEU 4.0 2.0 - - - -
172E ALA* 3.9 7.4 - - + -
185E PHE* 3.5 45.1 - - + -
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Residues in contact with TYR 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E ALA* 3.6 28.0 - - + -
124E PRO 3.4 15.3 - - - -
125E HIS* 3.9 5.2 - - + -
142E ARG* 3.0 51.0 + - + -
143E LEU* 1.3 77.9 - - - +
145E PHE* 1.3 62.3 + - - +
152E ASN* 3.6 19.7 - - - +
155E CYS* 3.1 18.8 - - - -
157E VAL* 3.9 5.9 - - + +
158E LEU* 3.6 33.8 + - + -
170E LEU* 2.9 25.5 + - + +
171E ILE* 4.0 12.8 - - + -
172E ALA* 2.7 37.6 + - - +
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Residues in contact with PHE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E ILE* 3.8 22.4 - - + -
51E LEU* 4.2 2.7 - - + -
110E LYS* 3.7 19.7 - - + -
111E PRO* 3.7 39.7 - - + -
124E PRO* 3.7 24.5 + - + -
125E HIS* 4.5 0.2 - - - -
126E ILE* 3.9 17.0 - - + -
143E LEU* 3.8 20.6 - - + -
144E TYR* 1.3 75.9 - - - +
146E ASP* 1.4 58.3 + - - +
147E ASP* 3.5 16.2 - - - +
148E GLU* 3.0 22.1 + - + +
152E ASN* 3.1 16.8 + - - +
171E ILE* 4.3 1.6 - - - -
172E ALA 4.0 1.8 - - - -
183E TYR* 3.7 31.0 - + + -
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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