Contacts of the helix formed by residues 746 - 763 (chain A) in PDB entry 4FYT
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 746 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A THR 4.7 11.9 + - - -
429A TRP 5.8 1.4 + - - -
430A ASN* 4.9 9.7 - - - +
744A PRO* 3.5 1.2 - - - +
745A GLU* 1.3 80.6 - - + +
747A LEU* 1.3 65.6 + - - +
748A MET* 2.9 32.6 + - - +
749A ASP* 3.1 32.4 + - - +
750A GLN* 2.9 23.5 + - - +
1021A SO4 5.2 0.4 + - - -
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Residues in contact with LEU 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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376A SER* 3.7 24.7 - - - +
380A GLU* 4.5 0.9 - - + +
428A THR 5.6 1.4 + - - -
429A TRP* 3.8 54.6 - - + +
431A LEU* 3.9 13.2 - - + -
745A GLU 3.8 2.6 + - - -
746A ASN* 1.3 75.1 - - - +
748A MET* 1.3 84.4 + - + +
750A GLN* 3.1 15.0 + - - +
751A TYR* 3.0 58.3 + - + +
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Residues in contact with MET 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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429A TRP 4.0 15.5 - - - +
430A ASN* 5.3 9.6 - - + +
433A ASP* 6.4 1.3 - - - -
434A LEU* 3.8 32.3 - - + -
691A GLN* 4.9 11.2 - - - +
692A TYR* 3.3 31.2 - - + +
693A MET* 5.8 4.3 - - - -
746A ASN* 2.9 14.2 + - - +
747A LEU* 1.3 103.6 - - + +
749A ASP* 1.3 60.0 + - - +
751A TYR* 3.1 19.4 + - + +
752A SER* 2.8 24.1 + - - -
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Residues in contact with ASP 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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690A ARG* 4.7 9.7 - - - +
691A GLN* 5.0 10.6 - - - +
733A PHE* 3.9 7.4 - - + -
744A PRO* 3.6 20.6 - - + +
746A ASN* 3.1 30.7 + - + +
748A MET* 1.3 76.1 - - - +
750A GLN* 1.3 59.5 + - - +
752A SER* 3.3 6.8 + - - -
753A GLU* 2.9 28.9 + - - +
1021A SO4 4.2 11.7 + - - +
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Residues in contact with GLN 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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376A SER* 2.6 32.0 + - - -
743A ILE* 3.8 13.3 - - + +
744A PRO* 3.1 42.1 + - + +
745A GLU 3.4 16.2 + - - -
746A ASN 2.9 14.5 + - - +
747A LEU* 3.3 14.3 - - - +
749A ASP* 1.3 75.3 - - - +
751A TYR* 1.3 66.9 + - + +
753A GLU* 3.3 6.1 + - - +
754A VAL* 3.2 26.1 + - - +
791A ASN* 3.0 19.9 + - - +
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Residues in contact with TYR 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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376A SER* 4.5 3.1 - - - -
377A SER* 3.4 39.5 - - - -
380A GLU* 2.5 36.0 + - - +
434A LEU* 4.7 3.6 - - + -
692A TYR* 3.4 37.2 - + + -
747A LEU* 3.0 33.7 + - + +
748A MET* 3.1 33.2 + - + +
750A GLN* 1.3 78.2 - - + +
752A SER* 1.3 65.4 + - - +
754A VAL* 3.3 10.5 + - + +
755A ASN* 3.0 25.1 + - - +
791A ASN* 5.9 1.6 - - - -
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Residues in contact with SER 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG 2.8 29.4 + - - -
691A GLN 4.0 1.9 + - - -
692A TYR* 3.8 19.3 + - - +
695A TRP* 5.3 2.6 - - - +
729A LEU* 4.3 9.0 - - - +
733A PHE* 3.8 13.1 - - - -
748A MET 2.8 13.6 + - - -
749A ASP* 3.3 11.0 + - - -
751A TYR* 1.3 76.2 - - - +
753A GLU* 1.3 58.1 + - - +
755A ASN* 3.3 4.9 + - - +
756A ALA* 2.8 30.3 + - - +
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Residues in contact with GLU 753 (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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733A PHE* 3.5 34.7 - - + -
737A THR* 3.6 15.1 - - - +
740A TRP* 3.3 26.0 - - - -
742A GLU 4.6 2.1 - - - +
743A ILE* 4.0 12.5 - - - +
744A PRO* 3.2 20.0 - - + +
749A ASP 2.9 12.7 + - - +
750A GLN* 3.5 9.8 - - - +
752A SER* 1.3 76.9 - - - +
754A VAL* 1.3 62.3 + - - +
756A ALA* 3.3 2.6 + - - +
757A ILE* 3.0 29.0 + - + +
791A ASN* 5.6 0.9 + - - +
792A LEU* 3.9 21.3 - - - +
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Residues in contact with VAL 754 (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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750A GLN 3.2 15.1 + - - +
751A TYR* 3.3 11.9 + - + +
753A GLU* 1.3 76.4 - - + +
755A ASN* 1.3 60.8 + - - +
757A ILE* 3.3 9.1 + - - +
758A SER* 2.9 28.7 + - - -
791A ASN* 3.4 39.3 - - + +
792A LEU* 4.4 8.1 - - + -
794A SER* 6.4 1.3 - - - -
795A THR* 4.5 17.8 - - + +
1017A SO4 5.3 7.9 - - - +
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Residues in contact with ASN 755 (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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692A TYR* 3.4 23.9 + - - -
695A TRP* 5.0 7.5 - - + +
696A GLU* 2.8 35.3 + - - +
699A LEU* 3.8 21.0 - - + +
751A TYR 3.0 14.6 + - - +
752A SER* 3.8 5.6 - - - +
754A VAL* 1.3 79.4 - - - +
756A ALA* 1.3 57.1 + - - +
758A SER* 3.8 6.5 - - - -
759A THR* 2.8 36.2 + - - -
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Residues in contact with ALA 756 (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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726A VAL* 3.8 15.8 - - + +
729A LEU* 3.7 30.7 - - + +
730A PHE* 4.2 11.3 - - - +
733A PHE* 3.8 11.7 - - + -
752A SER 2.8 18.6 + - - +
753A GLU 3.3 5.1 + - - +
755A ASN* 1.3 76.1 - - - +
757A ILE* 1.3 57.0 + - + +
760A ALA* 2.9 32.4 + - - +
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Residues in contact with ILE 757 (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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730A PHE* 4.3 3.8 - - + -
733A PHE* 6.1 0.2 - - + -
740A TRP* 3.8 37.5 - - + -
753A GLU* 3.0 21.1 + - - +
754A VAL* 3.7 5.8 - - - +
756A ALA* 1.3 73.6 - - + +
758A SER* 1.3 66.7 + - - +
761A CYS* 3.0 23.0 + - - +
768A CYS* 3.3 21.0 - - - -
771A MET* 4.1 14.1 - - + -
772A VAL* 4.4 8.5 - - + -
792A LEU* 3.8 33.7 - - + -
795A THR* 3.7 21.3 - - + +
796A VAL* 5.2 1.6 - - + -
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Residues in contact with SER 758 (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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754A VAL* 2.9 18.8 + - - -
755A ASN* 3.8 10.8 - - - -
757A ILE* 1.3 76.3 - - - +
759A THR* 1.3 60.0 + - - +
761A CYS* 4.0 0.7 - - - +
762A SER* 3.0 40.1 + - - -
795A THR* 3.4 22.7 + - - -
799A ASN* 4.7 4.4 + - - +
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Residues in contact with THR 759 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695A TRP* 4.4 7.2 - - + -
699A LEU* 3.4 39.1 - - + +
722A LEU* 4.5 8.3 - - + -
726A VAL* 3.9 28.2 - - + +
755A ASN 2.8 25.2 + - - -
758A SER* 1.3 71.7 - - - +
760A ALA* 1.3 64.2 + - - +
762A SER* 4.6 1.1 - - - -
763A ASN* 2.9 45.8 + - - +
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Residues in contact with ALA 760 (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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726A VAL* 3.6 16.3 - - + +
730A PHE* 3.7 26.5 - - + -
756A ALA 2.9 23.9 + - - +
757A ILE 3.8 0.9 - - - +
759A THR* 1.3 72.9 - - - +
761A CYS* 1.3 58.1 + - - +
763A ASN 3.8 0.2 - - - -
764A GLY 3.1 8.1 + - - -
765A VAL* 2.8 45.4 + - + +
768A CYS* 3.8 7.0 - - + -
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Residues in contact with CYS 761 (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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757A ILE* 3.0 11.9 + - - +
760A ALA* 1.3 74.0 - - - +
762A SER* 1.3 65.2 + - - +
763A ASN 3.1 2.3 + - - -
764A GLY 3.4 0.3 + - - -
768A CYS* 2.1 59.9 - - - -
769A GLU* 2.5 31.2 - - - +
772A VAL* 3.5 23.1 - - - -
799A ASN* 3.6 25.0 - - - +
803A GLN* 5.2 1.2 + - - -
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Residues in contact with SER 762 (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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715A TYR* 5.1 3.6 + - - -
719A LYS* 3.8 18.0 + - - +
758A SER* 3.0 25.2 + - - -
759A THR* 4.6 0.9 - - - -
761A CYS* 1.3 76.6 - - - +
763A ASN* 1.3 70.4 + - - +
764A GLY 3.5 0.6 + - - -
799A ASN* 4.0 11.1 + - - -
1020A SO4 4.9 2.3 + - - -
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Residues in contact with ASN 763 (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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699A LEU* 6.0 0.2 - - - +
715A TYR* 4.8 3.8 + - - -
719A LYS* 3.4 53.6 - - - +
720A ASN* 5.6 0.3 - - - +
722A LEU* 3.5 32.6 - - - +
723A LYS* 3.5 28.0 - - - +
759A THR* 2.9 35.4 + - - +
760A ALA 3.8 0.9 - - - +
761A CYS 3.1 0.6 - - - -
762A SER* 1.3 87.8 - - - +
764A GLY* 1.3 60.5 + - - +
765A VAL 3.7 1.6 - - - -
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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
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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