Contacts of the strand formed by residues 139 - 145 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K ILE 3.7 0.5 - - - +
129K SER* 3.2 5.8 - - - -
130K LEU* 2.9 48.7 + - + +
135K ILE* 4.4 17.7 - - + -
137K ILE* 4.3 5.6 - - + +
138K HIS* 1.4 76.7 - - - +
140K HIS* 1.3 60.9 + - - +
141K THR* 4.1 0.7 + - - +
189K ILE* 4.1 19.1 - - + -
197K PHE* 3.7 49.4 - - + -
319L ALA* 6.1 2.2 - - + -
330L ARG 5.0 0.2 - - - +
332L PRO* 4.1 23.1 - - + -
336L LEU* 5.0 8.5 - - + -
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Residues in contact with HIS 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K ILE 3.3 5.3 + - - +
129K SER* 3.5 14.3 + - - -
138K HIS* 3.5 36.3 + + - -
139K LEU* 1.3 72.0 - - - +
141K THR* 1.3 61.8 + - - +
197K PHE* 3.2 11.1 - - - +
198K PHE* 2.9 45.5 + - + +
199K ASP* 5.1 1.3 - - - -
200K PHE* 3.4 49.3 + + + -
311L ARG* 4.0 15.5 + - - -
313L ARG* 4.3 14.6 + - - -
470L ILE* 4.4 13.3 - - + +
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Residues in contact with THR 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K ASN* 3.9 1.2 - - - -
128K ILE* 3.0 47.9 + - + +
130K LEU* 6.2 1.1 - - + -
139K LEU 5.5 0.9 - - - +
140K HIS* 1.3 78.2 - - - +
142K ARG* 1.3 75.0 + - - +
170K LEU* 2.9 14.6 - - - +
185K PHE* 4.4 10.3 - - + -
187K ILE* 4.4 16.8 - - + -
195K THR* 3.8 1.6 - - + +
196K VAL 2.9 22.1 + - - -
197K PHE* 3.8 15.9 - - + -
198K PHE* 3.7 9.2 - - - -
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Residues in contact with ARG 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122K MET* 3.4 36.6 - - - +
125K HIS* 3.5 24.5 + - + -
126K ILE 3.4 6.1 - - - +
127K ASN* 3.6 15.2 + - - +
128K ILE* 5.2 0.4 - - - -
141K THR* 1.3 88.4 + - - +
143K LEU* 1.3 59.6 + - - +
144K TYR* 2.9 42.4 + - + -
157K VAL* 3.5 26.7 - - - +
170K LEU* 3.4 27.5 - - + +
185K PHE* 3.6 6.8 - - - -
198K PHE* 3.7 16.5 - - + -
339L ILE* 4.5 3.6 - - - +
342L SER* 3.7 4.6 + - - -
344L SER* 3.7 5.3 - - - -
345L GLU* 2.8 34.4 + - - -
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Residues in contact with LEU 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K LEU* 3.8 24.0 - - + -
104K TRP* 4.7 6.7 - - + -
125K HIS* 3.1 8.1 - - - +
126K ILE* 2.9 43.4 + - + +
128K ILE* 4.0 19.3 - - + +
142K ARG* 1.3 69.8 - - - +
144K TYR* 1.3 69.7 + - - +
145K PHE* 3.7 32.1 - - + -
170K LEU 3.8 3.1 - - - -
172K ALA* 3.8 13.9 - - + -
185K PHE* 3.6 37.0 - - + -
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Residues in contact with TYR 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123K ALA* 3.7 28.3 - - + -
124K PRO 3.6 16.2 - - - -
125K HIS* 3.8 2.9 - - + -
142K ARG* 2.9 53.8 + - + -
143K LEU* 1.3 77.6 - - - +
145K PHE* 1.3 58.2 + - - +
152K ASN* 3.6 19.7 - - - +
155K CYS* 3.2 18.6 - - - -
157K VAL* 3.5 10.7 - - + +
158K LEU* 3.7 32.8 + - + -
170K LEU* 2.9 20.3 + - + +
171K ILE* 4.2 12.1 - - + -
172K ALA* 2.6 38.6 + - - +
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Residues in contact with PHE 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K ILE* 3.8 23.8 - - + -
51K LEU* 4.4 2.9 - - + -
110K LYS* 3.8 12.1 - - + -
111K PRO* 3.9 31.4 - - + -
124K PRO* 3.6 34.2 + - + -
125K HIS* 4.5 2.7 - - - -
126K ILE* 4.0 9.4 - - + -
143K LEU* 3.7 26.7 - - + -
144K TYR* 1.3 75.7 - - - +
146K ASP* 1.4 60.4 + - - +
147K ASP* 3.5 17.0 - - - +
148K GLU* 3.1 10.9 + - + +
152K ASN* 2.8 29.8 + - - +
171K ILE* 4.3 1.8 - - - -
172K ALA 3.9 2.2 - - - -
183K TYR* 3.6 30.5 - + + -
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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