Contacts of the helix formed by residues 549 - 560 (chain E) in PDB entry 6T8B
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 549 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542E MET* 3.7 5.6 - - - +
548E ARG* 1.3 83.4 + - + +
550E LEU* 1.3 60.4 + - - +
551E ALA* 4.0 15.8 - - + +
552E GLY* 2.6 41.8 + - - -
553E PHE 3.1 9.4 + - - -
620E ARG 5.9 0.2 - - - +
621E ALA* 3.7 12.1 - - + +
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Residues in contact with LEU 550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E ARG* 3.9 7.6 - - - +
542E MET* 3.6 23.1 - - + -
549E ASN* 1.3 74.2 - - - +
551E ALA* 1.3 57.3 + - - +
553E PHE* 3.2 4.8 + - + -
554E ASN* 2.9 28.1 + - + +
587E LEU* 3.3 48.5 - - + +
588E PRO 3.8 2.9 - - - -
589E THR* 3.6 35.9 - - + +
621E ALA 3.3 12.1 + - - +
622E ALA 4.4 0.4 - - - +
623E GLY* 3.9 18.2 - - - +
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Residues in contact with ALA 551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E ASN* 3.2 16.4 - - + +
550E LEU* 1.3 77.6 - - - +
552E GLY* 1.3 58.0 + - - +
554E ASN* 3.2 9.1 + - - +
555E ARG* 2.9 35.9 + - + +
558E LYS* 4.9 4.6 + - - +
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Residues in contact with GLY 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547E VAL* 3.7 24.5 - - - +
549E ASN* 2.6 29.0 + - - -
551E ALA* 1.3 75.5 - - - +
553E PHE* 1.3 58.8 + - - +
555E ARG* 3.1 26.8 + - - +
556E LYS* 3.8 4.2 + - - +
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Residues in contact with PHE 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541E LEU* 3.5 45.5 - - + -
542E MET* 3.5 25.8 - - + -
545E MET* 4.7 15.3 - - + -
547E VAL* 3.7 13.8 - - + +
549E ASN 3.1 6.1 + - - -
550E LEU* 3.2 7.4 + - + +
552E GLY* 1.3 75.1 - - - +
554E ASN* 1.3 61.9 + - - +
556E LYS* 3.6 18.9 + - + +
557E VAL* 3.8 22.4 - - + +
568E THR 6.1 0.9 - - - -
570E PRO* 5.9 1.3 - - + -
586E THR 5.1 1.6 - - - -
587E LEU* 3.6 45.8 - - + -
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Residues in contact with ASN 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E GLU* 5.8 4.8 - - - +
550E LEU* 2.9 17.3 + - + +
551E ALA* 3.5 9.8 - - - +
552E GLY 3.2 0.2 - - - -
553E PHE* 1.3 75.8 - - - +
555E ARG* 1.3 63.9 + - - +
556E LYS 3.1 2.5 - - - -
557E VAL* 3.2 18.0 + - - +
558E LYS* 2.9 43.8 + - + +
586E THR* 3.5 28.4 + - + +
587E LEU 5.6 3.6 + - - +
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Residues in contact with ARG 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551E ALA* 2.9 26.3 + - - +
552E GLY* 3.1 18.1 + - - +
554E ASN* 1.3 75.9 - - - +
556E LYS* 1.3 67.1 + - - +
558E LYS* 3.5 27.3 - - - +
559E ASP* 2.9 45.4 + - - +
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Residues in contact with LYS 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545E MET* 3.8 31.3 + - + -
547E VAL* 3.7 27.0 - - + +
552E GLY 4.3 6.4 + - - +
553E PHE* 3.8 15.9 - - + +
554E ASN 3.1 0.8 - - - -
555E ARG* 1.3 81.8 - - - +
557E VAL* 1.3 56.6 + - + +
559E ASP* 3.0 4.7 + - - +
560E ALA* 2.5 40.1 + - - +
567E LEU* 3.5 28.4 - - + +
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Residues in contact with VAL 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E PHE* 3.8 20.2 - - + +
554E ASN* 3.3 24.7 - - - +
556E LYS* 1.3 78.1 - - + +
558E LYS* 1.3 57.1 + - - +
559E ASP 3.5 0.2 - - - -
560E ALA* 3.9 10.9 - - + +
561E GLU* 3.8 24.4 + - - +
567E LEU* 5.3 12.8 - - + +
586E THR* 3.2 46.2 + - - +
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Residues in contact with LYS 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551E ALA* 4.9 5.3 + - - +
554E ASN* 2.9 42.9 + - - +
555E ARG* 3.5 41.1 - - - +
557E VAL* 1.3 76.2 - - - +
559E ASP* 1.3 70.2 + - - +
561E GLU* 4.1 12.8 + - - +
562E GLU* 3.9 11.6 + - - +
586E THR* 5.4 1.3 - - - +
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Residues in contact with ASP 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555E ARG* 2.9 38.9 + - - +
556E LYS* 3.0 3.6 + - - +
558E LYS* 1.3 85.6 - - - +
560E ALA* 1.3 54.5 + - - +
561E GLU 3.0 5.8 - - - -
562E GLU* 2.9 29.0 - - + +
563E ALA* 2.8 32.6 + - + +
565E THR* 4.4 0.6 + - - -
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Residues in contact with ALA 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556E LYS 2.5 21.9 + - - +
557E VAL* 3.9 13.5 - - + +
558E LYS 3.6 0.2 - - - -
559E ASP* 1.3 70.5 - - - +
561E GLU* 1.3 60.2 + - + +
564E GLY* 3.1 6.6 - - - -
565E THR* 2.6 59.4 + - - +
567E LEU* 4.5 10.1 - - + +
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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