Contacts of the helix formed by residues 549 - 563 (chain F) in PDB entry 6T8G
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542F MET* 3.7 13.4 - - - +
547F VAL* 3.3 8.0 - - - +
548F ARG* 1.3 85.9 - - + +
550F LEU* 1.3 62.0 + - - +
551F ALA* 3.4 21.1 - - - +
552F GLY* 2.9 27.7 + - - -
553F PHE* 3.3 15.6 - - - +
621F ALA* 3.8 22.4 - - + +
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Residues in contact with LEU 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538F ARG* 4.4 11.2 - - - +
542F MET* 3.9 4.5 - - - -
549F ASN* 1.3 76.0 - - - +
551F ALA* 1.3 59.4 + - - +
553F PHE* 3.3 16.3 - - + +
554F ASN* 3.0 52.3 + - - +
587F LEU* 3.7 39.7 - - + +
588F PRO 4.6 1.8 - - - +
589F THR* 4.4 13.7 - - - +
621F ALA 3.5 14.8 + - - +
622F ALA 4.3 4.3 - - - +
623F GLY* 3.8 26.5 - - - +
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Residues in contact with ALA 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549F ASN* 3.0 21.5 + - - +
550F LEU* 1.3 80.3 - - - +
552F GLY* 1.3 63.7 + - - +
553F PHE 3.4 0.2 + - - -
554F ASN* 3.6 5.3 + - - +
555F ARG* 3.6 28.5 + - - +
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Residues in contact with GLY 552 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547F VAL* 3.7 12.3 - - - -
549F ASN* 2.9 16.0 + - - -
551F ALA* 1.3 72.2 - - - +
553F PHE* 1.3 58.9 + - - +
555F ARG* 3.5 9.5 + - - +
556F LYS* 2.9 31.5 + - - +
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Residues in contact with PHE 553 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541F LEU* 3.7 31.4 - - + -
542F MET* 4.9 10.1 - - + -
545F MET* 4.2 17.5 - - + -
547F VAL* 3.4 25.9 - - + +
549F ASN 3.3 15.2 + - - +
550F LEU* 3.1 27.5 + - + +
552F GLY* 1.3 77.6 - - - +
554F ASN* 1.3 65.6 + - - +
556F LYS* 3.3 8.2 + - + +
557F VAL* 2.9 39.6 + - + +
584F LEU* 4.5 18.6 - - + -
585F SER 4.7 3.8 - - - -
587F LEU* 3.6 27.4 - - + -
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Residues in contact with ASN 554 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550F LEU* 3.0 40.4 + - - +
551F ALA* 4.2 4.9 - - - +
552F GLY 3.4 0.2 - - - -
553F PHE* 1.3 83.9 - - - +
555F ARG* 1.3 59.3 + - + +
557F VAL* 3.3 5.3 - - - +
558F LYS* 2.9 37.3 + - + +
586F THR* 4.1 10.5 - - + -
587F LEU 3.5 30.8 + - - +
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Residues in contact with ARG 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436F LYS* 4.4 21.2 - - - +
551F ALA* 3.6 17.0 + - - +
552F GLY* 3.5 12.0 + - - +
553F PHE 3.3 0.4 - - - -
554F ASN* 1.3 78.2 - - + +
556F LYS* 1.3 57.2 + - - +
558F LYS* 3.4 3.4 + - - +
559F ASP* 2.9 42.9 + - - +
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Residues in contact with LYS 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545F MET* 5.2 21.5 - - + -
547F VAL* 5.0 14.6 - - + -
552F GLY 2.9 19.1 + - - +
553F PHE* 3.7 9.4 - - + +
555F ARG* 1.3 76.8 - - - +
557F VAL* 1.3 61.6 + - + +
559F ASP* 3.4 5.9 + - - +
560F ALA* 2.9 38.2 + - + +
567F LEU* 5.4 12.6 - - + +
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Residues in contact with VAL 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553F PHE* 2.9 31.5 + - + +
554F ASN* 3.3 22.0 - - - +
556F LYS* 1.3 80.8 - - + +
558F LYS* 1.3 74.5 + - + +
560F ALA* 3.4 5.9 + - - +
561F GLU* 2.8 25.5 + - - +
565F THR 4.9 3.0 - - - +
566F PRO* 6.2 0.7 - - + -
567F LEU* 4.9 9.2 - - + +
584F LEU* 3.8 39.0 - - + -
585F SER 4.6 9.4 - - - +
586F THR* 5.3 1.1 - - - -
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Residues in contact with LYS 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F ASN* 2.9 23.6 + - + +
555F ARG* 4.2 3.6 - - - +
556F LYS 3.2 0.2 - - - -
557F VAL* 1.3 88.4 - - + +
559F ASP* 1.3 61.9 + - - +
560F ALA 3.2 0.2 - - - -
561F GLU* 3.5 33.0 - - + +
562F GLU* 2.9 34.7 + - + +
584F LEU 5.7 2.6 + - - -
585F SER* 5.6 1.7 - - - +
586F THR* 3.7 33.9 - - + +
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Residues in contact with ASP 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555F ARG* 2.9 29.6 + - - +
556F LYS* 3.9 5.4 - - - +
558F LYS* 1.3 77.6 - - - +
560F ALA* 1.3 57.9 + - - +
562F GLU* 3.6 11.6 + - - +
563F ALA* 2.9 26.0 + - - +
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Residues in contact with ALA 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556F LYS* 2.9 27.4 + - + +
557F VAL* 3.7 6.7 - - - +
559F ASP* 1.3 74.9 - - - +
561F GLU* 1.3 54.1 + - - +
563F ALA* 3.2 9.6 - - - +
564F GLY 2.9 8.7 + - - -
565F THR* 2.7 46.0 + - - +
567F LEU* 4.2 15.0 - - + -
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Residues in contact with GLU 561 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F VAL* 2.8 17.9 + - + +
558F LYS* 3.2 35.5 + - - +
560F ALA* 1.3 77.3 - - - +
562F GLU* 1.3 70.4 + - - +
564F GLY* 2.9 18.6 + - - +
565F THR 4.2 9.2 + - - +
566F PRO* 5.9 6.7 - - + -
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Residues in contact with GLU 562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558F LYS* 2.9 19.3 + - - +
559F ASP* 3.7 10.9 - - - +
561F GLU* 1.3 85.3 - - - +
563F ALA* 1.3 56.8 + - - +
564F GLY 3.2 3.1 + - - -
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Residues in contact with ALA 563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559F ASP 2.9 19.3 + - - +
560F ALA* 3.2 13.7 - - - +
561F GLU 3.2 0.4 - - - -
562F GLU* 1.3 74.5 - - - +
564F GLY* 1.3 59.8 + - - +
565F THR* 3.6 8.2 + - - +
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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