Contacts of the helix formed by residues 754 - 769 (chain A) in PDB entry 6NFJ
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 ALA 754 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A GLU* 4.0 27.8 - - + +
494A SER* 4.9 1.1 - - - +
751A ASN* 3.0 39.9 + - + +
753A TYR* 1.3 77.6 - - - +
755A ASP* 1.3 65.5 + - - +
756A SER* 4.6 1.6 - - - +
757A HIS* 3.3 13.1 + - + +
758A TRP* 3.3 10.7 - - - -
55B PHE* 4.8 0.2 - - - -
56B ASN* 5.6 1.1 - - - -
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Residues in contact with ASP 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ALA* 1.3 67.2 - - - +
756A SER* 1.3 57.6 + - - +
757A HIS 3.0 5.2 - - - -
758A TRP* 2.9 27.7 + - - +
759A ARG* 3.2 16.2 + - - +
52B GLU* 3.0 33.2 - - + +
53B TYR* 3.7 5.6 - - + -
54B ILE* 3.8 5.6 - - - -
55B PHE* 3.1 45.3 - - - -
56B ASN* 3.5 19.5 + - - +
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Residues in contact with SER 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 4.3 16.2 + - - -
754A ALA* 3.3 1.2 - - - +
755A ASP* 1.3 77.6 - - - +
757A HIS* 1.3 60.3 + - - +
759A ARG* 3.2 26.9 + - - +
760A ALA* 3.4 22.0 + - - +
763A ARG* 5.0 0.9 + - - -
833A HIS* 3.4 39.7 - - - +
56B ASN* 4.3 10.1 + - - +
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Residues in contact with HIS 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 3.4 23.6 + - - -
430A THR* 3.2 24.9 - - - -
749A PRO* 3.6 24.3 - - + +
750A ALA* 3.7 3.3 + - + +
751A ASN* 3.0 30.3 + - + +
754A ALA* 3.3 13.2 + - + +
755A ASP 3.0 0.8 - - - -
756A SER* 1.3 81.0 - - - +
758A TRP* 1.3 59.9 + - - +
760A ALA* 3.5 4.6 + - - +
761A ALA* 2.9 27.5 + - - +
831A VAL* 4.1 4.3 - - - +
832A MET* 3.4 33.0 - - + +
833A HIS* 3.2 19.4 + - + +
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Residues in contact with TRP 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A GLU* 4.5 9.6 - - - -
749A PRO* 3.7 26.9 - - + -
751A ASN 4.3 1.1 - - - -
752A PRO* 3.2 47.7 + - + +
754A ALA 3.3 23.8 - - - -
755A ASP* 2.9 14.8 + - - +
757A HIS* 1.3 74.8 - - - +
759A ARG* 1.3 66.1 + - - +
761A ALA* 3.1 18.6 + - - +
762A GLU* 3.7 4.5 + - - +
30B ARG* 3.4 35.9 + - - +
53B TYR* 3.4 49.5 - + + -
54B ILE* 6.1 0.2 - - + -
55B PHE* 4.8 4.3 - + - -
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Residues in contact with ARG 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A ASP 3.2 13.4 + - - +
756A SER* 3.2 33.0 + - - +
758A TRP* 1.3 76.4 - - - +
760A ALA* 1.3 62.5 + - - +
761A ALA 3.4 0.2 + - - -
762A GLU 3.6 1.0 + - - -
763A ARG* 3.3 24.8 + - - +
833A HIS* 5.5 1.6 - - - -
30B ARG 3.4 23.1 - - - +
31B SER* 3.5 22.2 - - - +
32B TYR 4.4 2.0 - - - +
33B PHE* 3.4 29.1 - - - +
52B GLU* 3.4 29.7 - - - +
53B TYR* 4.0 23.3 - - + +
56B ASN* 4.9 1.6 - - - +
58B TYR* 5.8 0.4 + - - -
100B GLY 2.6 31.1 + - - +
101B ALA* 5.2 0.8 - - - +
102B SER* 3.6 16.0 + - - +
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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
----------------------------------------------------------
756A SER 3.4 17.7 + - - +
757A HIS* 3.5 3.5 + - - +
758A TRP 3.2 0.6 - - - -
759A ARG* 1.3 76.2 - - - +
761A ALA* 1.3 64.0 + - - +
762A GLU 3.3 0.2 - - - -
763A ARG* 3.3 36.7 - - - +
764A PHE* 3.0 18.9 + - - +
831A VAL* 3.3 22.8 - - + +
832A MET 4.5 7.4 - - - +
833A HIS* 4.7 0.2 - - - +
847A ILE* 3.7 7.7 - - + +
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Residues in contact with ALA 761 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ALA* 3.8 7.1 - - - +
748A GLU* 4.3 9.0 - - - +
749A PRO* 4.1 24.9 - - + -
757A HIS 2.9 13.9 + - - +
758A TRP* 3.1 13.0 + - - +
760A ALA* 1.3 78.9 - - - +
762A GLU* 1.3 63.8 + - + +
764A PHE* 3.6 4.9 + - - +
765A LEU* 3.5 21.6 + - - +
831A VAL* 3.7 10.8 - - - -
30B ARG* 4.4 9.0 - - - +
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Residues in contact with GLU 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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746A TRP* 4.4 7.1 - - - -
758A TRP 3.7 1.5 + - - +
759A ARG 3.6 3.3 + - - +
761A ALA* 1.3 75.5 - - - +
763A ARG* 1.3 60.6 + - - +
764A PHE 3.2 0.4 - - - -
765A LEU* 3.0 20.8 + - - +
766A GLN* 2.8 41.0 + - + +
875A TRP* 3.0 33.0 + - - -
878A ARG* 5.2 3.2 + - - -
28B ALA* 5.6 6.3 - - + +
30B ARG* 3.7 50.7 + - + +
31B SER* 4.0 19.1 - - - +
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Residues in contact with ARG 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A SER 5.0 0.8 + - - -
759A ARG* 3.3 22.8 + - - +
760A ALA* 3.3 36.5 + - - +
762A GLU* 1.3 77.7 - - - +
764A PHE* 1.3 56.0 + - - +
766A GLN* 4.4 6.5 - - + -
767A PHE* 3.0 52.4 + - + -
785A ALA 5.9 0.7 - - - +
789A TYR* 3.5 40.9 + - + -
833A HIS* 3.3 22.4 + - - -
845A ARG 2.7 17.7 + - - +
846A ASP 3.0 27.1 + - - -
847A ILE* 4.1 2.7 - - + +
31B SER* 4.2 9.3 + - - -
100B GLY* 4.4 21.2 - - - -
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Residues in contact with PHE 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A HIS* 6.1 3.4 - + - -
745A ASP* 3.3 31.9 - - + -
746A TRP 4.6 1.3 - - - -
747A ALA* 3.4 22.7 - - + -
760A ALA 3.0 9.3 + - - +
761A ALA 3.7 7.2 - - - +
762A GLU 3.2 0.2 - - - -
763A ARG* 1.3 75.9 - - - +
765A LEU* 1.3 68.9 + - + +
767A PHE* 3.2 5.8 + - - +
768A GLU* 3.0 35.2 + - + +
829A ARG* 4.6 12.1 - - + -
831A VAL* 3.9 10.3 - - + -
845A ARG* 3.5 24.7 - - - -
847A ILE* 3.6 17.8 - - + +
849A PHE* 3.5 35.4 - + - -
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Residues in contact with LEU 765 (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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745A ASP 3.8 21.3 - - - +
746A TRP* 3.5 41.7 - - + -
747A ALA* 4.2 7.6 - - + +
761A ALA 3.5 11.4 + - - +
762A GLU* 3.0 37.1 + - - +
764A PHE* 1.3 84.1 - - + +
766A GLN* 1.3 58.6 + - - +
768A GLU* 4.5 0.4 - - - +
769A ILE* 2.7 46.9 + - + +
770A ALA 3.3 5.4 + - - -
872A LEU* 4.9 3.4 - - + -
875A TRP* 4.2 15.4 - - + +
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Residues in contact with GLN 766 (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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762A GLU* 2.8 31.8 + - + +
763A ARG* 3.9 8.1 - - + +
765A LEU* 1.3 73.5 - - - +
767A PHE* 1.3 59.5 + - + +
768A GLU 3.1 0.2 - - - -
770A ALA* 3.3 22.3 - - - +
771A TRP* 3.1 26.0 + - - -
774A GLU* 4.0 6.7 + - - +
783A PRO* 3.7 17.2 - - - +
785A ALA* 4.2 17.8 - - + +
786A MET* 4.1 9.8 - - + +
875A TRP* 3.6 28.9 - - - +
879A ASN* 4.5 4.2 + - - -
880A TYR* 5.5 0.4 + - - -
27B ARG* 5.7 1.0 - - - +
28B ALA* 3.4 34.2 - - + +
31B SER* 5.3 1.8 - - - -
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Residues in contact with PHE 767 (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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763A ARG* 3.0 48.2 + - + +
764A PHE 3.2 4.4 + - - +
766A GLN* 1.3 76.5 - - + +
768A GLU* 1.3 56.4 + - - +
771A TRP* 3.7 14.3 - - - +
785A ALA 4.9 0.4 - - - -
786A MET* 3.9 37.9 - - + -
789A TYR* 4.0 10.3 - + + -
790A ILE* 3.8 32.1 - - + -
841A TYR* 2.2 55.3 + + - +
844A ASP* 3.9 15.9 - - + -
845A ARG* 3.8 35.4 - - + +
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Residues in contact with GLU 768 (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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695A ASN* 4.0 22.5 - - + +
742A LEU* 5.7 2.1 - - - +
743A HIS* 4.8 12.6 - - + +
764A PHE* 3.0 35.8 + - + +
765A LEU* 4.1 1.6 - - - +
766A GLN 3.1 0.4 - - - -
767A PHE* 1.3 78.8 - - - +
769A ILE* 1.3 72.7 + - + +
771A TRP* 3.9 10.3 - - - +
772A PHE* 4.4 2.4 + - - +
845A ARG* 5.1 3.4 - - - +
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Residues in contact with ILE 769 (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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742A LEU* 4.2 16.3 - - + +
743A HIS 3.4 22.7 - - - +
744A ALA* 3.6 24.0 - - + -
745A ASP 4.7 2.0 - - - +
765A LEU* 2.7 33.5 + - + +
768A GLU* 1.3 72.9 - - + +
770A ALA* 1.3 64.6 + - - +
771A TRP 3.0 2.6 + - - -
772A PHE* 3.1 12.6 + - - -
773A ALA* 3.2 21.5 + - + +
777A PHE* 6.0 1.3 - - + -
823A LEU* 5.1 9.0 - - + -
872A LEU* 4.3 11.0 - - + -
875A TRP* 3.4 30.5 - - + -
876A VAL* 5.3 3.4 - - + -
880A TYR* 4.6 1.8 - - + -
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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