Contacts of the helix formed by residues 742 - 751 (chain A) in PDB entry 6A5T
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 742 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A ASP* 2.7 49.2 + - - +
738A LEU* 3.4 35.5 - - + +
739A LYS* 3.8 23.5 - - + +
740A ASP 3.0 5.3 - - - +
741A LEU* 1.3 90.1 - - + +
743A ASN* 1.3 80.7 + - - +
744A VAL 3.6 4.2 + - - -
745A LYS* 4.0 4.4 + - + +
746A GLN* 3.1 18.4 + - - +
192C TRP* 4.5 5.6 - - - +
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Residues in contact with ASN 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A LYS* 5.5 0.5 + - - -
663A PHE* 4.1 12.3 - - + -
664A SER 2.6 30.0 + - - +
665A ILE* 3.4 12.8 - - + +
666A GLY 4.1 1.6 - - - +
669A ASP* 2.4 25.8 + - + +
741A LEU 3.4 11.9 - - - +
742A ASN* 1.3 80.0 + - - +
744A VAL* 1.3 58.1 + - - +
745A LYS 3.0 1.3 - - - -
746A GLN* 2.3 40.5 + - - +
747A MET* 2.9 15.6 + - + +
1069B PHE* 4.7 6.9 - - - -
1084B GLN 5.8 0.2 + - - -
192C TRP* 5.4 4.2 - - - +
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A ILE* 4.5 15.5 - - + -
669A ASP* 3.9 28.0 - - + +
670A ALA* 4.7 3.1 - - + +
738A LEU* 5.3 2.9 - - + -
742A ASN* 3.6 5.6 + - - +
743A ASN* 1.3 74.1 - - - +
745A LYS* 1.3 63.6 + - - +
747A MET* 3.2 9.7 + - - +
748A VAL* 3.0 27.3 + - + +
758A ASN* 6.1 0.4 - - + -
759A ILE* 3.5 35.9 - - + -
762A MET* 4.1 25.4 - - + -
1018B PRO* 5.2 9.6 - - + -
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Residues in contact with LYS 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735A GLU* 4.7 25.5 + - + +
736A MET* 5.4 3.0 + - - +
738A LEU* 4.0 23.5 + - + +
739A LYS 3.2 21.1 - - - +
740A ASP* 3.2 26.3 + - - +
742A ASN* 4.0 14.9 + - + +
743A ASN 3.0 0.6 - - - -
744A VAL* 1.3 79.5 - - - +
746A GLN* 1.3 63.9 + - - +
748A VAL* 4.6 5.4 - - + +
749A SER* 3.2 28.2 + - - +
759A ILE* 5.1 5.3 - - + +
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Residues in contact with GLN 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A CYS* 4.8 6.5 - - - -
533A ARG* 3.7 28.8 + - - +
534A LYS* 3.1 42.3 + - - +
537A LEU* 6.0 2.6 - - - +
663A PHE* 4.1 5.7 - - + -
740A ASP 3.7 7.5 + - - +
741A LEU* 3.0 35.9 + - - +
742A ASN 3.1 16.0 + - - +
743A ASN* 2.3 35.2 + - - +
745A LYS* 1.3 71.6 - - - +
747A MET* 1.3 61.1 + - - +
749A SER* 3.8 1.1 - - - -
750A ALA* 3.0 21.7 + - - +
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Residues in contact with MET 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530A CYS* 3.5 22.4 - - - -
663A PHE* 4.0 20.2 - - + -
665A ILE* 5.6 8.3 - - + -
743A ASN* 2.9 11.6 + - + +
744A VAL* 4.1 8.5 - - + +
746A GLN* 1.3 76.6 - - - +
748A VAL* 1.3 54.3 + - + +
750A ALA* 2.7 8.4 + - - +
751A GLY* 2.4 35.9 + - - -
752A SER* 3.4 12.0 + - - +
753A LYS* 4.6 6.1 - - - +
1014B PRO* 5.1 3.8 - - + -
1015B HIS* 3.1 46.2 - - + +
1018B PRO* 3.7 34.1 - - + -
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Residues in contact with VAL 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735A GLU* 5.3 8.5 - - + +
744A VAL* 3.0 21.3 + - + +
745A LYS* 4.3 3.1 - - - +
747A MET* 1.3 73.6 - - + +
749A SER* 1.3 57.8 + - - +
751A GLY* 2.6 25.6 + - - +
753A LYS 4.3 7.6 - - - +
754A GLY* 4.5 3.8 - - - -
755A SER* 3.2 45.1 - - - +
756A PHE* 4.5 2.7 - - + +
758A ASN* 5.7 0.7 - - + -
759A ILE* 3.7 19.5 - - + -
1018B PRO* 6.2 2.7 - - + -
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Residues in contact with SER 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A ARG* 4.3 13.3 + - - -
617A VAL* 5.7 2.4 - - - +
619A ASP* 2.9 22.3 - - - +
621A LYS* 5.4 1.7 + - - -
745A LYS* 3.2 25.7 + - - -
746A GLN* 3.9 3.4 - - - -
747A MET 3.2 0.4 - - - -
748A VAL* 1.3 80.0 - - - +
750A ALA* 1.3 56.6 + - - +
751A GLY 3.7 0.2 + - - -
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Residues in contact with ALA 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 3.2 16.4 - - + +
530A CYS* 4.1 19.7 - - - +
533A ARG* 3.6 30.0 - - + +
619A ASP* 3.9 6.2 - - + +
620A LYS 3.7 12.6 + - - -
746A GLN 3.0 15.0 + - - +
747A MET* 2.7 17.0 + - - +
749A SER* 1.3 73.9 - - - +
751A GLY* 1.3 60.8 + - - -
752A SER 3.1 3.1 + - - +
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Residues in contact with GLY 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A LEU* 3.9 3.3 - - - +
620A LYS* 3.9 26.7 + - - +
747A MET 2.4 18.3 + - - -
748A VAL 2.6 17.8 + - - -
749A SER 4.7 0.2 - - - -
750A ALA* 1.3 67.5 - - - +
752A SER* 1.3 64.2 + - - +
753A LYS* 3.3 6.7 - - - -
754A GLY 5.9 0.4 - - - -
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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