Contacts of the helix formed by residues 724 - 733 (chain B) in PDB entry 5TDF
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 GLU 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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697B PHE* 3.5 23.0 - - + -
715B VAL* 5.2 0.4 - - + -
717B GLY* 3.4 6.6 - - - -
718B GLU 3.0 32.7 + - - +
720B GLY 4.6 0.9 - - - +
722B THR 3.1 0.8 + - - -
723B GLU* 1.3 79.8 + - - +
725B TYR* 1.3 62.8 + - - +
727B ILE* 3.0 34.5 + - + +
728B CYS* 3.6 0.6 + - - -
742B CYS* 4.8 2.7 - - - -
744B CYS* 3.8 13.5 - - - -
775B LYS* 2.7 40.0 + - + +
779B LEU* 3.6 26.9 - - + +
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Residues in contact with TYR 725 (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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722B THR* 3.2 36.1 + - + +
723B GLU 3.1 1.2 + - - -
724B GLU* 1.3 75.6 - - - +
726B LYS* 1.3 62.5 + - + +
727B ILE 3.2 0.2 - - - -
728B CYS* 3.2 14.3 + - + +
729B ARG* 3.0 21.0 + - - +
769B SER* 2.7 43.3 + - - -
774B ALA* 3.8 12.0 + - - +
775B LYS* 3.7 23.3 - - + +
778B ALA* 3.5 31.2 - - + -
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Residues in contact with LYS 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 5.9 4.0 - - - +
696B THR* 5.0 6.1 + - - +
698B MET* 3.6 32.9 - - + +
722B THR* 4.9 4.3 - - - +
723B GLU* 2.7 50.9 + - - +
725B TYR* 1.3 78.9 - - + +
727B ILE* 1.3 56.0 + - - +
729B ARG* 3.4 16.0 + - - +
730B GLY 2.9 23.2 + - - -
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Residues in contact with ILE 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B PHE* 4.7 7.9 - - + -
698B MET* 4.2 14.6 - - - +
701B VAL* 4.5 11.7 - - + -
715B VAL* 4.2 34.8 - - + -
723B GLU 5.1 1.1 - - - +
724B GLU* 3.0 24.3 + - + +
726B LYS* 1.3 74.9 - - - +
728B CYS* 1.3 66.2 + - - +
730B GLY 3.3 0.2 + - - -
731B ILE* 3.1 24.4 + - + +
736B LEU* 3.8 7.5 - - + +
740B ILE* 3.9 29.8 - - + -
742B CYS* 5.1 1.8 - - - -
779B LEU* 4.2 8.7 - - + -
784B VAL* 4.0 20.0 - - + -
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Residues in contact with CYS 728 (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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725B TYR* 3.2 24.1 + - + +
727B ILE* 1.3 77.4 - - - +
729B ARG* 1.3 61.5 + - - +
731B ILE* 3.4 4.9 + - - +
732B LYS* 3.1 23.4 + - - +
778B ALA* 3.6 34.5 - - - -
779B LEU* 3.7 27.1 - - - -
782B ALA* 3.7 20.6 - - + +
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Residues in contact with ARG 729 (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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725B TYR 3.0 13.0 + - - +
726B LYS* 3.6 17.4 - - - +
728B CYS* 1.3 77.0 - - - +
730B GLY* 1.3 57.0 + - - +
732B LYS* 3.2 13.0 + - - +
733B GLU* 2.9 62.8 + - + +
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Residues in contact with GLY 730 (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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698B MET* 4.1 8.3 - - - -
726B LYS 2.9 15.1 + - - -
727B ILE 3.3 2.6 + - - -
729B ARG* 1.3 77.1 - - - +
731B ILE* 1.3 59.5 + - - +
733B GLU* 3.5 10.3 + - - -
734B GLY 3.3 1.9 + - - -
735B ARG* 2.9 32.8 + - - -
736B LEU* 3.0 21.3 + - - -
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Residues in contact with ILE 731 (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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727B ILE* 3.1 19.9 + - + +
728B CYS* 3.8 4.3 - - - +
730B GLY* 1.3 73.2 - - - +
732B LYS* 1.3 68.2 + - - +
734B GLY* 3.0 13.5 + - - -
736B LEU* 3.7 30.3 - - + +
738B LYS 6.0 0.7 - - - +
740B ILE* 4.3 10.5 - - + -
782B ALA 3.4 25.1 - - - +
783B GLY* 4.4 5.8 - - - +
784B VAL* 3.3 38.4 - - + +
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Residues in contact with LYS 732 (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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728B CYS 3.1 18.2 + - - +
729B ARG* 3.2 11.0 + - - +
731B ILE* 1.3 78.4 - - - +
733B GLU* 1.3 83.5 + - - +
734B GLY 3.3 1.4 + - - -
782B ALA* 6.3 0.4 - - + -
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Residues in contact with GLU 733 (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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729B ARG* 2.9 57.3 + - - +
730B GLY* 3.9 10.6 - - - +
731B ILE 3.2 0.2 - - - -
732B LYS* 1.3 96.8 + - - +
734B GLY* 1.3 59.5 + - - +
735B ARG* 3.4 12.2 + - + +
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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
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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