Contacts of the strand formed by residues 149 - 154 (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 GLY 149 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C LEU* 4.4 5.8 - - - -
148C THR* 1.3 81.5 - - - +
150C ILE* 1.3 60.3 + - - -
151C VAL* 3.9 4.4 - - - +
162C VAL 4.0 1.0 - - - +
163C PRO 3.7 0.2 - - - -
164C ILE* 2.8 33.0 + - - +
292C LEU* 3.4 10.1 - - - -
295C ASN* 3.3 21.1 - - - -
297C VAL* 5.1 0.7 - - - -
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLY* 1.3 73.0 - - - -
151C VAL* 1.3 63.9 + - - +
152C MET* 3.5 2.4 + - + +
161C THR* 3.7 20.4 - - + -
162C VAL 3.7 2.2 - - - -
163C PRO* 3.9 18.6 - - + -
277C THR* 4.0 11.4 - - + -
280C SER* 3.6 31.2 - - - -
281C ILE* 3.7 26.5 - - + -
292C LEU* 3.6 19.5 - - + +
295C ASN 3.6 3.4 + - - -
296C THR* 3.2 31.5 - - + +
297C VAL 3.0 17.2 + - - -
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Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA* 3.7 27.4 - - + +
140C SER* 3.2 22.4 - - - +
141C LEU* 3.9 34.8 - - + -
149C GLY 4.8 1.1 - - - +
150C ILE* 1.3 74.6 - - - +
152C MET* 1.3 61.8 + - - +
153C ASP 3.7 1.3 + - - +
160C HIS 3.8 0.3 - - - +
161C THR* 3.4 5.4 - - - -
162C VAL 3.0 33.6 + - - +
164C ILE* 5.7 1.3 - - + -
297C VAL* 3.3 23.1 - - + +
299C SER* 4.1 13.7 - - - +
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Residues in contact with MET 152 (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* 3.5 4.0 + - + +
151C VAL* 1.3 69.9 - - - +
153C ASP* 1.3 58.8 + - - +
154C SER* 3.9 8.2 + - - +
159C THR* 3.3 28.0 - - + -
160C HIS 3.7 2.7 - - - +
161C THR* 3.6 22.0 - - + +
273C ILE* 3.6 39.3 - - + +
276C THR* 4.9 0.9 - - - +
277C THR* 4.3 17.3 - - - +
296C THR* 4.9 5.8 - - + -
297C VAL 2.8 7.7 + - - +
298C LEU* 3.5 29.5 - - + -
299C SER* 2.8 29.6 + - - +
303C THR* 4.7 6.2 - - + +
312C MET* 5.1 5.6 - - + -
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Residues in contact with ASP 153 (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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108C PRO* 4.4 2.1 - - - +
136C GLN* 2.9 39.1 - - - +
137C ALA* 4.5 9.5 + - + -
151C VAL* 3.7 10.1 + - + -
152C MET* 1.3 72.4 - - - +
154C SER* 1.3 62.4 + - - +
155C GLY 3.8 9.7 + - - -
158C VAL 4.6 0.3 - - - +
159C THR* 3.2 1.7 - - - +
160C HIS* 2.5 67.7 + - + +
299C SER* 3.4 18.1 + - - +
300C GLY* 4.8 0.9 - - - -
338C VAL* 5.3 1.5 - - - +
402C MG 4.0 7.1 - - - -
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Residues in contact with SER 154 (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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152C MET* 3.9 8.0 + - - +
153C ASP* 1.3 75.5 + - - +
155C GLY* 1.3 61.1 + - - +
159C THR* 3.1 30.7 - - - +
260C LEU* 5.7 2.4 - - - +
299C SER 3.4 4.7 + - - +
300C GLY* 3.2 22.8 - - - -
302C THR* 3.0 26.0 + - - +
303C THR* 3.4 21.3 - - - +
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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
------------------------------------------------------------
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