Contacts of the helix formed by residues 782 - 801 (chain B) in PDB entry 5TBY
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 782 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724B ILE* 3.3 11.1 - - - +
779B GLU 5.2 1.8 + - - -
780B ARG 2.7 13.7 + - - -
781B LEU* 1.3 79.1 - - - +
783B ARG* 1.3 87.5 + - - +
784B ILE 3.2 2.9 + - - -
785B ILE 3.7 4.3 + - - -
786B THR* 4.4 7.9 - - - +
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Residues in contact with ARG 783 (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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724B ILE* 4.0 13.0 - - + +
727B PRO* 5.6 12.1 - - + -
782B SER* 1.3 90.7 + - - +
784B ILE* 1.3 68.5 + - + +
786B THR* 3.7 1.1 - - - -
787B ARG* 2.8 49.3 + - - +
126D ASP* 2.1 60.1 + - - +
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Residues in contact with ILE 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ARG* 3.9 15.7 - - - +
724B ILE* 3.8 28.6 - - + +
732B GLU* 4.5 2.0 - - - +
782B SER 3.2 0.8 + - - -
783B ARG* 1.3 85.0 - - + +
785B ILE* 1.3 61.6 + - - +
787B ARG* 3.5 10.0 - - - -
788B ILE* 2.8 37.6 + - + +
128D GLY* 5.4 0.2 - - - -
132D ASP* 3.2 39.3 - - + +
133D PHE* 3.7 45.5 - - + +
136D GLY* 5.3 1.1 - - - -
137D LEU* 6.3 1.6 - - + -
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Residues in contact with ILE 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B ARG* 3.2 18.6 - - + +
722B TYR 4.4 0.4 - - - +
723B ARG* 2.7 42.8 - - + +
724B ILE* 3.9 11.2 - - + -
781B LEU* 3.2 45.3 - - + -
782B SER 3.7 4.2 + - - +
783B ARG 3.5 0.6 - - - -
784B ILE* 1.3 74.9 - - - +
786B THR* 1.3 60.2 + - - +
788B ILE* 2.7 27.1 - - + +
789B GLN* 3.2 12.1 - - - +
156D VAL 5.3 4.9 - - - +
160D LEU* 3.6 30.1 - - + +
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Residues in contact with THR 786 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778B ASP 5.5 0.2 + - - -
781B LEU 2.8 22.2 + - - -
782B SER* 4.0 6.8 + - - -
783B ARG 3.5 6.1 + - - -
784B ILE 3.3 0.2 - - - -
785B ILE* 1.3 77.4 - - - +
787B ARG* 1.3 55.4 + - - +
788B ILE 3.3 0.2 - - - -
789B GLN* 3.6 12.6 - - - +
790B ALA* 2.7 36.9 + - + +
88D THR* 3.9 27.8 - - + -
161D GLY* 3.6 17.5 - - - -
162D GLU* 3.9 19.9 + - + +
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Residues in contact with ARG 787 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B ARG* 2.8 44.9 + - - +
784B ILE* 3.1 9.6 + - - +
786B THR* 1.3 77.3 - - + +
788B ILE* 1.3 58.8 + - - +
790B ALA* 3.9 7.1 - - + +
791B GLN* 2.9 45.4 + - + +
86D ASN* 4.8 17.4 + - - +
126D ASP 3.2 11.2 + - - -
127D THR* 0.4 118.8 + - - +
128D GLY* 2.4 18.1 + - - +
133D PHE* 3.6 18.8 - - + -
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Residues in contact with ILE 788 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723B ARG* 3.5 19.1 - - - +
784B ILE* 2.8 18.5 + - + +
785B ILE* 2.7 25.8 - - + +
787B ARG* 1.3 72.9 - - - +
789B GLN* 1.3 72.4 + - + +
791B GLN* 3.2 7.6 + - - +
792B SER* 2.9 28.9 + - - -
133D PHE* 3.1 33.9 - - + -
137D LEU* 5.7 14.6 - - + -
156D VAL* 5.0 10.3 - - + +
157D LEU* 4.2 25.4 - - + -
188D PHE* 6.5 1.3 - - + -
192D ILE* 5.1 3.7 - - - +
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Residues in contact with GLN 789 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785B ILE* 3.2 19.3 + - - +
786B THR* 3.6 10.8 - - - +
788B ILE* 1.3 88.1 - - + +
790B ALA* 1.3 52.2 + - - +
792B SER* 3.2 11.0 + - - -
793B ARG* 2.8 38.3 + - + +
156D VAL 4.6 2.4 + - - -
157D LEU* 3.6 22.8 + - - +
160D LEU 2.5 30.6 + - - -
161D GLY* 3.5 2.3 - - - -
162D GLU* 2.9 31.8 + - + +
163D ARG* 2.9 18.0 + - - +
164D LEU* 4.2 15.7 - - + +
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Residues in contact with ALA 790 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B THR* 2.7 25.4 + - + +
787B ARG* 3.9 10.1 - - + +
789B GLN* 1.3 73.7 - - - +
791B GLN* 1.3 59.8 + - + +
793B ARG* 3.0 14.3 + - - +
794B GLY* 2.8 25.5 + - - -
86D ASN* 5.0 13.0 + - + -
87D PRO 4.7 16.4 - - - +
88D THR* 5.6 3.6 - - + -
162D GLU* 5.4 4.9 - - - +
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Residues in contact with GLN 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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787B ARG* 2.9 32.1 + - + +
788B ILE* 3.5 6.1 - - - +
790B ALA* 1.3 74.6 - - + +
792B SER* 1.3 51.5 + - - +
794B GLY* 3.1 4.5 + - - +
795B VAL* 2.7 40.1 + - + +
86D ASN* 5.4 11.0 - - + +
128D GLY 6.0 1.2 - - - -
129D THR 4.9 0.6 + - - -
133D PHE* 3.0 38.4 - - - -
192D ILE* 3.9 15.0 - - + +
193D MET* 1.9 51.5 - - + +
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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
----------------------------------------------------------
788B ILE 2.9 13.6 + - - -
789B GLN* 3.2 16.1 + - - -
791B GLN* 1.3 73.1 - - - +
793B ARG* 1.3 57.3 + - - +
795B VAL* 3.4 11.7 - - - +
796B LEU* 2.9 31.5 + - - +
164D LEU* 4.0 25.8 - - - +
168D GLU* 5.5 1.6 + - - +
172D LEU* 4.0 19.0 - - - +
192D ILE* 5.0 6.6 - - - +
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Residues in contact with ARG 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789B GLN* 2.8 27.7 + - + +
790B ALA* 3.0 18.8 + - - +
792B SER* 1.3 76.9 - - - +
794B GLY* 1.3 50.2 + - - +
796B LEU* 3.6 8.2 - - - +
797B ALA* 2.8 39.1 + - - +
81D ARG* 3.8 30.6 + - - +
89D GLN* 4.0 16.2 + - - +
162D GLU* 2.5 45.6 + - - +
163D ARG 4.4 10.6 + - - -
164D LEU* 4.5 12.8 - - - -
168D GLU* 4.3 17.4 + - - -
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Residues in contact with GLY 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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790B ALA 2.8 12.8 + - - -
791B GLN* 3.5 3.8 - - - -
793B ARG* 1.3 74.0 - - - +
795B VAL* 1.3 59.3 + - - +
797B ALA* 4.5 4.7 - - - -
798B ARG* 3.0 34.7 + - - +
81D ARG* 5.3 9.8 - - - +
86D ASN* 4.7 15.0 - - - -
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Residues in contact with VAL 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B GLN* 2.7 33.7 + - + +
792B SER* 3.3 12.3 + - - +
794B GLY* 1.3 76.1 - - - +
796B LEU* 1.3 67.2 - - - +
798B ARG* 3.5 7.0 + - - +
799B MET* 3.5 13.0 + - - +
172D LEU* 6.3 3.4 - - + -
192D ILE* 4.1 33.4 - - + +
195D SER* 5.1 22.8 + - - +
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Residues in contact with LEU 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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792B SER* 2.9 17.4 + - - +
793B ARG* 3.6 9.4 - - - +
795B VAL* 1.3 77.8 - - - +
797B ALA* 1.3 53.7 + - - +
799B MET* 3.0 8.9 + - - +
800B GLU* 2.8 53.7 + - + +
168D GLU* 3.8 31.2 - - + +
171D LYS* 5.5 12.6 - - + -
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Residues in contact with ALA 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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793B ARG 2.8 23.4 + - - +
794B GLY* 4.4 2.7 - - - +
796B LEU* 1.3 74.4 - - - +
798B ARG* 1.3 62.5 + - - +
799B MET 3.2 0.3 + - - -
800B GLU 4.4 2.0 - - - +
801B TYR* 3.4 30.8 + - + +
78D ASP* 3.2 30.3 - - + +
81D ARG* 4.5 12.3 - - + +
82D ALA* 6.1 2.2 - - - +
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Residues in contact with ARG 798 (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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794B GLY 3.0 23.2 + - - +
795B VAL* 3.8 5.2 - - - +
796B LEU 3.2 0.2 + - - -
797B ALA* 1.3 77.7 - - - +
799B MET* 1.3 58.7 + - + +
81D ARG 3.9 16.4 + - - -
82D ALA* 4.4 23.7 + - - +
84D GLY* 4.1 14.6 + - - -
86D ASN* 5.9 2.2 - - - +
195D SER* 5.0 13.3 + - - +
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Residues in contact with MET 799 (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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795B VAL 3.5 8.5 + - - +
796B LEU* 3.0 7.8 + - - +
798B ARG* 1.3 83.0 - - + +
800B GLU* 1.3 86.7 + - + +
801B TYR 3.7 1.9 + - - -
802B LYS* 5.2 2.1 + - - +
171D LYS* 6.0 8.7 - - - -
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Residues in contact with GLU 800 (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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796B LEU* 2.8 38.3 + - + +
797B ALA* 4.2 2.0 - - - -
799B MET* 1.3 114.9 - - + +
801B TYR* 1.3 62.3 + - - +
802B LYS* 2.7 61.1 + - - +
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Residues in contact with TYR 801 (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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797B ALA* 3.4 21.1 + - + +
799B MET 3.7 1.6 - - - -
800B GLU* 1.3 76.5 - - - +
802B LYS* 1.3 99.0 + - - +
803B LYS* 3.9 6.7 - - + +
804B LEU* 2.9 40.3 - - + +
805B LEU* 4.5 15.9 - - + -
61D PHE* 4.6 22.7 - + - -
75D GLN* 3.8 20.5 + - + +
78D ASP* 3.7 39.3 - - + -
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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