Contacts of the helix formed by residues 152 - 157 (chain B) in PDB entry 5T5I
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 ASN 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B CYS* 1.3 73.9 - - - +
153B PRO* 1.3 65.7 - - - +
154B MET 4.2 0.3 + - - -
155B HIS* 3.0 38.1 + - + +
156B ALA* 3.0 27.1 + - + +
185B ASP* 4.9 1.6 - - - +
187B ARG* 3.6 24.0 - - - +
189B THR* 3.4 28.4 - - + +
191B SER* 2.8 28.4 + - - -
9D ARG* 4.8 5.8 + - + +
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Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.8 31.0 - - + -
151B CYS* 3.4 12.1 - - + +
152B ASN* 1.3 86.9 - - - +
154B MET* 1.3 60.9 + - - +
157B HIS* 2.9 52.1 + - + +
158B PRO* 3.2 1.2 - - - -
160B HIS* 4.4 2.5 - - + -
161B MET* 4.0 23.1 - - + -
191B SER* 3.2 14.8 - - - +
287B MET* 4.1 16.4 - - + -
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ASN* 4.3 1.1 - - - +
153B PRO* 1.3 76.7 - - - +
155B HIS* 1.3 59.4 + - + +
158B PRO* 4.0 26.4 - - + +
161B MET* 4.0 16.6 - - - +
190B ASP* 4.0 21.3 - - + +
191B SER* 3.0 36.7 + - - +
194B LEU* 4.2 17.0 - - + -
11D ILE* 4.0 8.0 - - - +
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Residues in contact with HIS 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.7 18.4 - - - +
152B ASN* 3.0 36.7 + - - +
154B MET* 1.3 79.6 - - - +
156B ALA* 1.4 59.3 + - - +
157B HIS 4.0 0.2 - - - -
158B PRO* 4.4 3.1 - - - -
190B ASP* 2.8 35.8 + - + +
9D ARG* 4.4 8.7 - - + +
10D THR* 3.5 21.7 - - + +
11D ILE* 2.9 51.8 + - + +
12D TRP* 5.0 5.8 - + - -
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.9 3.6 - - - -
12B CYS* 4.0 10.7 - - - +
37B ILE* 4.8 5.9 - - - +
152B ASN* 3.0 18.4 + - + +
155B HIS* 1.4 76.3 - - - +
157B HIS* 1.3 81.4 + - + +
158B PRO* 3.6 7.4 - - - +
9D ARG* 4.0 31.0 - - + -
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Residues in contact with HIS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B CYS* 3.7 19.3 - - + -
13B GLY 4.2 0.4 - - - -
14B THR* 3.5 16.8 - - - +
151B CYS* 5.7 2.7 - - + +
152B ASN 5.7 0.2 - - - -
153B PRO* 2.9 20.8 + - + +
156B ALA* 1.3 88.5 + - + +
158B PRO* 1.4 67.5 - - - +
159B ARG 3.3 2.7 - - - -
160B HIS* 3.0 26.1 + - + +
161B MET 4.7 0.3 + - - -
287B MET* 3.5 40.9 + - + +
288B ARG 3.1 23.8 + - - -
289B GLY* 4.2 7.7 + - - -
396B MET* 3.5 20.9 - - + +
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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
------------------------------------------------------------
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