Contacts of the helix formed by residues 986 - 1017 (chain U) in PDB entry 5MQF
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 SER 986 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985U ARG* 3.8 28.7 - - - +
987U TYR* 3.8 29.6 - - - +
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Residues in contact with TYR 987 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961U VAL* 4.5 20.0 - - - +
986U SER* 3.8 27.1 - - - +
988U GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 988 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987U TYR* 3.8 28.9 - - - +
989U GLU* 3.8 26.5 - - - +
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Residues in contact with GLU 989 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
988U GLU* 3.8 28.7 - - - +
990U ASP* 3.8 27.4 - - - +
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Residues in contact with ASP 990 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989U GLU* 3.8 26.2 - - - +
991U MSE 3.8 29.2 - - - +
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Residues in contact with MSE 991 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990U ASP* 3.8 28.3 - - - +
992U GLU* 3.8 25.8 - - - +
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Residues in contact with GLU 992 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991U MSE 3.8 25.8 - - - +
993U ILE* 3.8 28.9 - - - +
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Residues in contact with ILE 993 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992U GLU* 3.8 29.4 - - - +
994U ALA* 3.8 25.1 - - - +
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Residues in contact with ALA 994 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993U ILE* 3.8 28.7 - - - +
995U GLU* 3.8 26.2 - - - +
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Residues in contact with GLU 995 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994U ALA* 3.8 25.1 - - - +
996U GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 996 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786U ASN* 4.6 18.8 - - - +
787U ARG* 4.7 5.6 - - - +
788U GLY* 4.3 15.7 - - - +
995U GLU* 3.8 25.8 - - - +
997U CYS* 3.8 29.8 - - - +
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Residues in contact with CYS 997 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788U GLY* 4.3 15.3 - - - +
996U GLY* 3.8 29.2 - - - +
998U PHE* 3.8 26.2 - - - +
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Residues in contact with PHE 998 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997U CYS* 3.8 29.2 - - - +
999U ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 999 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998U PHE* 3.8 28.5 - - - +
1000U HIS* 3.8 25.4 - - - +
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Residues in contact with HIS1000 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999U ARG* 3.8 26.2 - - - +
1001U ILE* 3.8 29.8 - - - +
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Residues in contact with ILE1001 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000U HIS* 3.8 29.6 - - - +
1002U LYS* 3.8 26.9 - - - +
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Residues in contact with LYS1002 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001U ILE* 3.8 29.2 - - - +
1003U LYS* 3.8 26.0 - - - +
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Residues in contact with LYS1003 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002U LYS* 3.8 26.5 - - - +
1004U ILE* 3.8 27.8 - - - +
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Residues in contact with ILE1004 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003U LYS* 3.8 26.0 - - - +
1005U PHE* 3.8 28.9 - - - +
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Residues in contact with PHE1005 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004U ILE* 3.8 26.7 - - - +
1006U THR* 3.8 28.7 - - - +
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Residues in contact with THR1006 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005U PHE* 3.8 25.4 - - - +
1007U GLN* 3.8 29.2 - - - +
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Residues in contact with GLN1007 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006U THR* 3.8 29.2 - - - +
1008U LEU* 3.8 26.7 - - - +
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Residues in contact with LEU1008 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007U GLN* 3.8 26.0 - - - +
1009U GLU* 3.8 28.9 - - - +
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Residues in contact with GLU1009 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008U LEU* 3.8 29.4 - - - +
1010U GLU* 3.8 25.6 - - - +
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Residues in contact with GLU1010 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009U GLU* 3.8 28.7 - - - +
1011U PHE* 3.8 25.8 - - - +
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Residues in contact with PHE1011 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010U GLU* 3.8 29.2 - - - +
1012U ARG* 3.8 26.5 - - - +
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Residues in contact with ARG1012 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011U PHE* 3.8 25.4 - - - +
1013U ALA* 3.8 28.9 - - - +
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Residues in contact with ALA1013 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012U ARG* 3.8 26.2 - - - +
1014U SER* 3.8 28.5 - - - +
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Residues in contact with SER1014 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013U ALA* 3.8 28.9 - - - +
1015U GLU* 3.8 25.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU1015 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014U SER* 3.8 25.8 - - - +
1016U LEU* 3.8 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU1016 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015U GLU* 3.8 26.9 - - - +
1017U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU1017 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016U LEU* 3.8 28.5 - - - +
1018U ARG* 3.8 29.2 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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