Contacts of the helix formed by residues 648 - 658 (chain B) 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 THR 648 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASP* 3.1 28.3 - - - +
12B ILE* 4.1 4.7 - - - +
641B ASN* 6.2 2.2 - - - +
645B LEU 5.5 2.5 - - - +
646B ARG* 2.9 12.4 + - - +
647B ILE* 1.3 84.1 - - - +
649B LYS* 1.3 64.3 + - - +
650B GLU* 3.1 29.1 + - + +
651B HIS* 3.3 19.5 + - + +
652B ILE* 4.0 2.3 + - - +
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Residues in contact with LYS 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 2.9 20.8 + - - +
10B ASP* 4.2 25.0 - - + +
11B THR 4.9 2.5 - - - +
12B ILE* 4.0 17.9 - - + +
13B THR* 5.6 4.2 - - - +
16B ASP* 3.2 34.7 + - - +
648B THR* 1.3 70.5 - - - +
650B GLU* 1.3 67.2 + - - +
651B HIS 3.1 0.6 + - - -
652B ILE* 3.1 11.2 + - + +
653B ARG* 2.9 23.8 + - - +
656B GLN* 5.6 2.2 - - - +
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Residues in contact with GLU 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 4.4 1.5 + - - +
648B THR* 3.1 17.9 - - - +
649B LYS* 1.3 77.8 - - - +
651B HIS* 1.3 69.9 + - + +
653B ARG* 2.8 36.3 + - - +
654B LYS* 3.0 39.5 + - - +
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Residues in contact with HIS 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B ARG* 4.4 5.2 - - + -
647B ILE* 3.7 24.3 - - + -
648B THR* 3.3 30.4 + - + -
649B LYS 3.1 0.8 - - - -
650B GLU* 1.3 78.8 - - + +
652B ILE* 1.3 68.5 + - - +
654B LYS* 3.2 16.5 + - - +
655B ILE* 2.9 29.8 + - - +
676B TYR* 4.2 20.8 + + + -
681B LEU* 4.7 14.4 - - + -
684B SER* 5.1 3.1 + - - -
686B VAL* 3.9 26.6 - - + +
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Residues in contact with ILE 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ILE* 4.7 3.6 - - + -
16B ASP* 3.3 59.2 - - + +
19B THR* 4.2 15.9 - - + -
20B VAL* 3.7 19.3 - - + -
647B ILE* 4.0 11.7 - - + -
648B THR 4.4 10.1 - - - +
649B LYS* 3.1 16.8 + - + +
651B HIS* 1.3 75.5 - - - +
653B ARG* 1.3 63.7 + - - +
655B ILE* 3.3 5.6 + - + +
656B GLN* 2.9 44.3 + - - +
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Residues in contact with ARG 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B LYS* 2.9 13.9 + - - +
650B GLU* 2.8 39.0 + - - +
652B ILE* 1.3 76.3 - - - +
654B LYS* 1.3 82.5 + - - +
656B GLN* 2.8 28.2 + - - +
657B GLN* 3.0 35.8 + - - +
661B ASP* 3.7 21.7 + - - +
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Residues in contact with LYS 654 (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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650B GLU* 3.0 38.7 + - - +
651B HIS* 3.7 17.2 + - + +
653B ARG* 1.3 89.3 - - - +
655B ILE* 1.3 66.3 + - - +
657B GLN* 2.9 17.1 + - - +
658B GLY* 2.9 12.3 + - - -
659B TYR 4.0 15.3 + - - +
660B ASP* 4.2 21.5 + - - +
661B ASP* 4.8 9.4 - - - +
676B TYR* 4.2 35.1 + - + +
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Residues in contact with ILE 655 (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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19B THR* 3.6 25.8 - - + +
20B VAL* 5.6 2.2 - - + -
23B ALA* 3.8 22.7 - - + +
651B HIS 2.9 19.0 + - - +
652B ILE* 3.8 7.2 - - + +
654B LYS* 1.3 75.8 - - - +
656B GLN* 1.3 61.1 + - - +
658B GLY* 3.7 7.9 + - - +
676B TYR* 3.2 45.5 - - + +
677B GLY* 4.5 5.2 - - - -
681B LEU* 4.4 28.3 - - + -
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Residues in contact with GLN 656 (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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16B ASP* 4.5 4.0 + - - -
19B THR* 4.5 14.5 + - + +
649B LYS* 5.6 2.8 - - - +
652B ILE* 2.9 44.1 + - + +
653B ARG* 2.8 26.5 + - - +
655B ILE* 1.3 78.4 - - - +
657B GLN* 1.3 63.7 + - + +
658B GLY* 3.4 0.5 + - - -
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Residues in contact with GLN 657 (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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653B ARG* 3.0 28.2 + - - +
654B LYS* 2.9 11.1 + - - +
656B GLN* 1.3 74.9 - - + +
658B GLY* 1.3 59.6 + - - +
659B TYR* 3.0 50.9 + - + +
661B ASP* 2.7 41.9 + - - +
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Residues in contact with GLY 658 (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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654B LYS 2.9 9.1 + - - -
655B ILE 3.7 7.4 + - - -
656B GLN 3.3 2.2 - - - -
657B GLN* 1.3 77.1 - - - +
659B TYR* 1.3 62.0 + - - +
675B VAL* 4.1 11.3 - - - +
676B TYR* 3.8 23.6 + - - -
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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