Contacts of the strand formed by residues 159 - 164 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C MET* 3.3 32.8 - - + -
153C ASP 3.2 6.3 - - - +
154C SER* 3.1 18.6 - - - +
158C VAL* 1.3 80.2 - - - +
160C HIS* 1.3 72.9 + - - +
161C THR* 4.7 2.0 - - - +
176C ARG* 3.5 0.3 - - - -
177C LEU* 2.8 56.7 + - + +
179C LEU* 3.1 20.6 + - - +
180C ALA* 4.6 1.2 + - - -
260C LEU* 5.6 2.6 - - - +
273C ILE* 4.7 2.9 - - + +
276C THR* 5.7 0.7 - - - +
302C THR* 5.0 0.2 - - - +
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Residues in contact with HIS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C HIS 5.5 0.2 + - - -
73C GLY* 5.8 1.6 - - - -
107C ALA* 3.2 26.9 - - + +
108C PRO* 3.6 43.4 + - + -
136C GLN* 4.3 2.7 + - - -
137C ALA* 5.9 0.2 - - + -
152C MET* 3.7 2.4 - - - +
153C ASP* 2.5 61.8 + - + +
158C VAL* 3.0 51.4 + - + +
159C THR* 1.3 76.4 - - - +
161C THR* 1.3 66.4 + - - +
162C VAL* 5.2 1.1 - - + -
175C LEU 3.5 7.9 - - - +
176C ARG* 3.8 20.0 + - + -
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Residues in contact with THR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 3.7 26.5 - - + -
151C VAL 3.4 7.9 - - - +
152C MET* 3.6 19.0 - - + +
159C THR* 4.7 2.3 - - - +
160C HIS* 1.3 82.2 + - - +
162C VAL* 1.3 66.1 + - - +
163C PRO* 3.8 0.7 - - - +
174C ILE* 3.3 4.9 - - - -
175C LEU* 2.8 44.0 + - - +
177C LEU* 6.1 0.5 - - - +
276C THR* 4.5 9.3 + - - -
277C THR* 4.7 9.4 - - - +
280C SER* 3.3 23.5 + - - +
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Residues in contact with VAL 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PRO* 3.9 27.6 - - + -
135C ILE* 5.3 4.0 - - + -
137C ALA* 3.9 21.1 - - + -
138C VAL* 5.0 6.1 - - + -
149C GLY 4.0 0.7 - - - +
150C ILE* 3.7 1.7 - - - -
151C VAL* 3.0 35.7 + - - +
161C THR* 1.3 81.0 - - - +
163C PRO* 1.3 75.0 - - - +
164C ILE* 3.7 19.1 + - + +
169C ALA* 5.3 3.4 - - + -
170C LEU 5.5 0.2 - - - +
174C ILE* 3.7 31.6 - - + -
374C PHE* 6.0 2.0 - - + -
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Residues in contact with PRO 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLY 3.7 4.9 - - - +
150C ILE* 3.9 15.9 - - + -
161C THR 3.8 6.7 - - - +
162C VAL* 1.3 94.4 - - + +
164C ILE* 1.3 61.2 + - - +
170C LEU* 3.8 25.3 + - + +
173C ALA* 3.4 41.3 - - + +
174C ILE* 4.1 3.6 - - + +
280C SER* 4.6 4.7 - - - -
284C CYS* 3.9 19.5 - - - -
292C LEU* 4.0 13.7 - - + -
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Residues in contact with ILE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C VAL* 3.9 26.0 - - + -
141C LEU* 3.2 35.2 - - + -
147C THR 3.7 8.7 - - - +
148C THR* 3.3 3.6 - - - +
149C GLY 2.8 38.9 + - - +
151C VAL* 5.7 1.8 - - + -
162C VAL* 4.2 11.9 - - + +
163C PRO* 1.3 76.3 - - - +
165C TYR* 1.3 61.5 + - - +
167C GLY* 3.2 9.9 - - - +
168C TYR 3.2 26.9 - - - +
169C ALA* 3.6 17.3 - - + +
170C LEU* 6.0 0.7 - - - -
288C ILE* 5.7 0.4 - - - -
292C LEU* 3.7 5.2 - - - +
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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