Contacts of the helix formed by residues 798 - 803 (chain B) in PDB entry 5IYB
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 ARG 798 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479A TRP* 6.2 4.5 - - - -
796B MET 3.3 2.8 + - - -
797B ASN* 1.3 63.4 - - - +
799B SER* 1.3 65.5 + - - +
801B VAL* 3.2 21.8 - - + +
802B ASP* 3.0 50.6 + - - -
948B GLN* 4.2 20.9 - - + +
949B TYR 2.5 34.7 + - - +
950B ARG* 3.3 36.8 - - - +
170C GLY 5.0 0.8 + - - -
171C LYS 4.1 3.6 + - - -
172C GLU 2.5 35.2 + - - -
173C HIS* 3.8 2.2 - - - +
174C ALA 4.8 0.2 - - - +
6K ALA* 5.1 6.5 + - - +
9K SER* 4.8 10.1 + - - -
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Residues in contact with SER 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ASN* 3.1 9.9 + - - -
798B ARG* 1.3 78.3 - - - +
800B ALA* 1.3 56.9 + - - +
802B ASP* 3.2 9.9 - - - +
803B ARG* 2.8 38.4 + - - +
949B TYR 4.2 0.4 + - - -
950B ARG* 4.0 4.5 - - - +
951B GLN* 3.1 43.7 + - - +
952B GLU* 4.3 1.9 + - - -
39C ILE* 5.7 0.2 - - - +
170C GLY 5.6 2.1 + - - -
174C ALA* 3.7 15.9 + - - +
177C ASN* 5.1 1.6 + - - -
8J PHE 4.5 0.2 - - - -
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Residues in contact with ALA 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797B ASN* 3.3 25.7 + - + +
798B ARG 3.1 0.8 - - - -
799B SER* 1.3 75.9 - - - +
801B VAL* 1.3 66.2 + - - +
802B ASP 3.1 0.9 + - - -
803B ARG* 3.1 7.9 + - - +
804B GLY 3.4 0.2 + - - -
805B PHE* 2.8 44.8 + - + +
964B ASP* 4.0 11.2 - - - +
8J PHE 3.4 22.6 + - - +
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Residues in contact with VAL 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796B MET* 4.8 7.9 - - - -
797B ASN 3.4 12.8 + - - +
798B ARG* 3.2 24.7 + - + +
800B ALA* 1.3 75.1 - - - +
802B ASP* 1.3 71.1 + - - +
804B GLY* 3.4 10.6 + - - -
805B PHE* 3.6 22.9 + - + +
807B ARG* 3.4 14.4 + - - +
928B ILE* 5.0 11.1 - - + +
929B PRO* 4.1 27.7 - - + +
948B GLN* 3.5 29.2 - - - +
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Residues in contact with ASP 802 (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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798B ARG* 3.0 47.2 + - - +
799B SER* 3.2 10.5 - - - +
801B VAL* 1.3 82.0 - - - +
803B ARG* 1.3 58.9 + - - +
804B GLY 2.9 10.1 + - - -
807B ARG* 3.0 19.5 + - - +
66C HIS* 3.8 4.7 + - - -
70C LEU* 4.7 2.6 - - - +
173C HIS* 3.7 30.1 + - - +
174C ALA* 3.7 22.4 + - + +
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Residues in contact with ARG 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B TYR* 4.8 0.9 - - - -
797B ASN* 5.9 0.2 - - - +
799B SER* 2.8 24.1 + - - +
800B ALA 3.1 4.6 + - - +
802B ASP* 1.3 70.9 - - - +
804B GLY* 1.3 55.9 + - - +
805B PHE 3.5 1.6 - - - -
951B GLN* 2.2 48.9 + - - +
39C ILE* 4.6 0.4 - - - +
66C HIS* 3.7 6.5 + - - -
70C LEU* 3.7 30.0 - - + +
174C ALA* 4.0 16.7 + - + +
177C ASN* 3.0 22.8 - - - +
179C THR 5.1 0.4 + - - -
4J PRO* 5.1 1.2 - - - +
5J VAL 4.7 2.9 - - - +
6J ARG* 4.9 13.4 - - + +
7J CYS 3.9 9.6 - - - -
8J PHE* 3.2 48.8 + - + +
9J THR 3.3 1.2 + - - -
10J CYS 3.1 23.4 + - - -
11J GLY* 3.6 12.6 - - - -
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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