Contacts of the strand formed by residues 139 - 143 (chain A) in PDB entry 3LJK
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 ASP 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.4 6.2 - - - +
138A THR* 1.3 101.8 + - - +
140A ILE* 1.3 65.5 + - - +
168A LYS* 3.3 23.4 - - - +
170A HIS* 2.8 25.2 + - + +
186A VAL 4.5 5.4 - - - +
187A VAL* 3.7 27.6 - - + +
188A ASP 5.2 0.2 + - - -
191A THR* 3.3 3.6 + - - +
192A THR* 3.3 14.2 + - + +
193A LEU 3.0 24.1 + - - -
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Residues in contact with ILE 140 (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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124A VAL* 4.3 0.7 - - + -
137A ILE* 4.0 10.1 - - + -
139A ASP* 1.3 81.0 - - - +
141A VAL* 1.3 65.7 + - - +
167A LEU* 3.9 24.9 - - + -
168A LYS 2.8 8.5 + - - +
169A VAL* 3.4 17.6 - - + -
170A HIS* 2.9 30.3 + - - +
193A LEU* 3.2 26.2 - - + +
195A ILE* 3.6 31.0 - - + -
271A SER* 5.0 0.4 - - - -
274A PHE* 3.9 36.1 - - + -
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Residues in contact with VAL 141 (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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140A ILE* 1.3 79.5 - - - +
142A ASN* 1.3 64.9 + - - +
143A ILE* 3.7 6.1 + - + +
170A HIS* 3.5 21.1 - - + +
172A VAL* 3.6 31.0 - - + -
180A LEU* 5.7 1.6 - - + -
183A ALA* 4.2 12.3 - - + -
184A LEU* 5.8 1.6 - - + -
187A VAL* 4.4 9.4 - - + -
192A THR* 3.6 22.4 - - + -
193A LEU 3.0 8.5 + - - -
194A LEU* 3.3 24.6 - - + +
195A ILE 2.8 26.6 + - - +
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Residues in contact with ASN 142 (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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140A ILE* 4.1 2.0 - - - +
141A VAL* 1.3 72.7 - - - +
143A ILE* 1.3 62.0 + - - +
144A GLY 4.2 4.8 + - - +
148A SER 3.0 27.1 + - - -
149A ASP* 4.4 2.8 + - - +
152A PRO* 5.2 2.6 - - - +
170A HIS 2.8 16.1 + - - +
171A PHE* 3.8 25.1 - - + -
172A VAL* 2.8 31.8 + - - +
195A ILE* 3.6 30.6 - - + +
197A ALA* 4.5 5.3 - - - +
234A ILE* 5.1 0.3 - - - +
268A ILE 4.8 6.5 + - - +
270A MSE 5.5 0.2 - - - +
271A SER* 4.0 21.2 + - - -
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Residues in contact with ILE 143 (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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141A VAL* 4.2 14.6 - - + +
142A ASN* 1.3 77.6 - - - +
144A GLY* 1.3 59.8 + - - +
172A VAL* 3.4 13.5 - - + +
180A LEU* 5.3 1.8 - - + -
194A LEU* 4.1 14.4 - - + -
195A ILE 2.8 19.4 + - - +
196A ILE* 3.8 11.6 - - + -
197A ALA* 2.9 30.1 + - - +
206A THR* 3.8 19.9 - - + +
209A ASN* 3.5 35.0 - - + +
210A SER* 4.3 8.1 - - - +
213A ALA* 3.9 27.8 - - + -
231A PHE* 4.7 0.9 - - + -
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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