Contacts of the strand formed by residues 159 - 164 (chain B) in PDB entry 5JLH
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 THR 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B MET* 3.3 33.7 - - + -
153B ASP 3.2 6.5 - - - +
154B SER* 3.1 18.2 - - - +
158B VAL* 1.3 80.2 - - - +
160B HIS* 1.3 71.8 + - - +
161B THR* 4.7 2.0 - - - +
176B ARG* 3.5 0.3 - - - -
177B LEU* 2.8 56.9 + - + +
179B LEU* 3.1 20.4 + - - +
180B ALA* 4.6 1.0 + - - -
260B LEU* 5.6 2.6 - - - +
273B ILE* 4.7 2.9 - - + +
276B THR* 5.7 0.4 - - - +
302B THR* 5.0 0.3 - - - +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B HIS 5.5 0.6 + - - -
73B GLY* 5.8 1.3 - - - -
107B ALA* 3.2 26.9 - - + +
108B PRO* 3.6 43.2 + - + -
136B GLN* 4.3 2.2 + - - -
137B ALA* 5.9 0.7 - - + -
152B MET* 3.7 2.4 - - - +
153B ASP* 2.5 62.5 + - + +
158B VAL* 3.0 51.2 + - + +
159B THR* 1.3 76.3 - - - +
161B THR* 1.3 66.9 + - - +
162B VAL* 5.3 0.7 - - + -
175B LEU 3.5 7.4 - - - +
176B ARG* 3.8 19.4 + - + -
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ILE* 3.7 26.7 - - + -
151B VAL 3.4 7.4 - - - +
152B MET* 3.6 18.9 - - - +
159B THR* 4.7 2.1 - - - +
160B HIS* 1.3 83.1 + - - +
162B VAL* 1.3 68.1 + - - +
163B PRO* 3.8 0.7 - - - +
174B ILE* 3.3 3.1 - - - -
175B LEU* 2.8 44.2 + - - +
177B LEU* 6.0 0.7 - - - +
276B THR* 4.5 9.1 + - - -
277B THR* 4.7 9.4 - - - +
280B SER* 3.4 23.8 - - - +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B PRO* 3.9 27.8 - - + -
135B ILE* 5.3 4.3 - - + -
137B ALA* 3.9 20.6 - - + -
138B VAL* 5.0 5.8 - - + -
149B GLY 4.0 0.9 - - - +
150B ILE* 3.7 1.9 - - - -
151B VAL* 3.0 35.1 + - - +
161B THR* 1.3 81.9 - - - +
163B PRO* 1.3 74.7 - - - +
164B ILE* 3.7 19.1 + - + +
169B ALA* 5.3 3.6 - - + -
170B LEU 5.5 0.2 - - - +
174B ILE* 3.8 31.2 - - + -
374B PHE* 5.9 2.7 - - + -
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Residues in contact with PRO 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLY 3.7 4.7 - - - +
150B ILE* 3.9 15.9 - - + -
161B THR 3.8 6.5 - - - +
162B VAL* 1.3 95.4 - - + +
164B ILE* 1.3 60.5 + - - +
169B ALA 4.3 0.2 - - - -
170B LEU* 3.8 25.4 + - + +
173B ALA* 3.4 41.7 - - + +
174B ILE* 4.1 3.1 - - + +
280B SER* 4.6 4.7 - - - -
284B CYS* 3.9 20.4 - - - -
292B LEU* 4.0 13.2 - - + -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL 4.5 2.0 - - - +
43A MET* 4.4 3.1 - - - -
138B VAL* 3.9 25.8 - - + -
141B LEU* 3.2 34.5 - - + -
147B THR 3.7 8.3 - - - +
148B THR* 3.3 3.6 - - - +
149B GLY 2.8 39.2 + - - +
151B VAL* 5.7 1.3 - - + -
162B VAL* 4.2 11.7 - - + +
163B PRO* 1.3 75.6 - - - +
165B TYR* 1.3 61.4 + - - +
167B GLY 3.2 9.2 - - - +
168B TYR 3.1 27.6 - - - +
169B ALA* 3.6 17.7 - - + +
170B LEU* 6.0 0.7 - - - -
288B ILE* 5.7 0.7 - - - -
292B LEU* 3.7 5.3 - - - +
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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