Contacts of the helix formed by residues 790 - 797 (chain B) in PDB entry 5M64
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 790 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789B ILE* 1.3 78.6 - - - +
791B LYS* 1.3 75.2 + - - +
792B SER* 3.1 17.0 - - - +
793B ALA* 3.2 17.6 + - + +
794B ASP* 3.1 21.3 + - - +
930B LYS* 4.4 1.1 - - - -
931B TRP 3.4 4.0 - - - -
932B PRO* 3.4 17.8 - - - +
933B THR* 3.2 28.2 - - - +
936B MET* 3.2 13.6 - - - +
944B GLN* 4.5 3.8 - - - +
945B PRO 3.9 1.4 - - - +
946B ASP* 2.8 32.3 + - + +
8J PHE* 5.4 2.9 - - - +
9J SER* 5.9 1.0 - - - -
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Residues in contact with LYS 791 (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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789B ILE 3.6 1.4 + - - -
790B ASN* 1.3 75.8 - - - +
792B SER* 1.3 63.3 + - - +
794B ASP* 3.3 3.7 + - - +
795B GLU* 2.9 30.5 + - + +
930B LYS* 3.7 31.4 - - + +
931B TRP 3.3 5.7 + - - -
932B PRO* 3.6 39.6 - - + +
213C GLY 3.9 9.1 + - - -
214C GLY 3.9 7.6 + - - -
215C ASP 2.8 36.0 + - - +
216C HIS* 3.7 14.1 - - + +
217C ALA 4.4 1.0 - - - +
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Residues in contact with SER 792 (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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790B ASN* 3.1 17.5 + - - +
791B LYS* 1.3 83.5 + - - +
793B ALA* 1.3 60.8 + - - +
795B GLU* 3.1 10.5 + - - +
796B ARG* 3.0 26.3 + - - +
932B PRO* 4.9 1.2 - - - +
933B THR* 4.4 14.7 + - - +
217C ALA* 4.4 18.5 - - - +
8J PHE* 4.2 19.0 - - - +
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Residues in contact with ALA 793 (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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789B ILE* 4.5 0.4 - - + -
790B ASN* 3.2 27.1 + - + +
792B SER* 1.3 79.4 - - - +
794B ASP* 1.3 57.8 + - - +
796B ARG* 3.1 4.9 + - - +
797B GLY 3.0 10.4 + - - -
798B PHE* 2.8 49.6 + - + +
946B ASP* 4.1 9.2 - - + -
8J PHE* 3.7 21.2 - - + +
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Residues in contact with ASP 794 (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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789B ILE* 5.4 3.6 - - + -
790B ASN 3.1 10.8 + - - +
791B LYS* 3.6 8.5 - - - +
793B ALA* 1.3 76.3 - - - +
795B GLU* 1.3 63.6 + - - +
797B GLY* 3.2 11.1 + - - -
798B PHE* 3.9 11.1 - - + +
910B THR* 4.4 8.7 - - - +
911B PRO* 3.1 40.6 - - + +
930B LYS* 3.5 28.6 - - - +
70L ARG* 4.7 8.0 - - - +
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Residues in contact with GLU 795 (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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791B LYS* 2.9 17.5 + - + +
792B SER* 3.1 11.2 + - - +
794B ASP* 1.3 82.1 + - - +
796B ARG* 1.3 59.1 + - - +
797B GLY 3.5 0.5 + - - -
99C HIS* 5.1 7.3 + - - +
103C LEU* 5.2 12.0 - - + +
215C ASP 4.8 0.3 - - - +
216C HIS* 3.3 33.8 + - - +
217C ALA* 3.4 31.2 - - + +
218C LYS* 2.4 38.0 + - - +
69L ALA 4.1 3.5 - - - +
70L ARG* 4.8 16.0 - - - +
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Residues in contact with ARG 796 (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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745B GLN* 4.7 4.7 + - - -
746B THR* 3.5 34.2 + - - +
769B PHE* 5.6 6.9 - - - +
792B SER 3.0 6.9 + - - +
793B ALA 3.1 6.8 + - - +
795B GLU* 1.3 76.1 - - - +
797B GLY* 1.3 70.1 + - - +
798B PHE* 4.0 10.5 - - - +
799B GLY 4.7 0.4 - - - +
99C HIS* 4.8 9.9 - - - -
103C LEU* 5.9 6.7 - - + -
217C ALA* 5.8 0.2 - - - +
4J PRO* 4.2 17.6 - - + +
5J VAL 4.1 8.3 - - - +
6J ARG 3.6 20.2 - - - +
7J CYS* 4.3 3.1 - - - +
8J PHE* 3.2 55.3 - - + +
49J MET* 3.5 21.0 - - - +
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Residues in contact with GLY 797 (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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745B GLN* 4.4 3.1 - - - -
746B THR* 3.4 19.2 - - - +
793B ALA 3.0 1.0 + - - -
794B ASP 3.2 7.7 + - - -
795B GLU 3.2 5.1 + - - -
796B ARG* 1.3 81.7 - - - +
798B PHE* 1.3 66.3 + - - +
799B GLY 3.0 4.9 + - - -
800B TYR* 3.2 28.4 + - - +
911B PRO* 5.5 1.6 - - - -
99C HIS* 5.6 3.6 - - - -
70L ARG* 6.0 1.1 - - - -
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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