Contacts of the helix formed by residues 544 - 560 (chain r) in PDB entry 6FF7
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 MET 544 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542r ALA* 4.5 4.6 - - - +
543r PRO* 1.3 81.1 - - + +
545r ARG* 1.3 60.7 + - - +
546r SER 3.6 1.6 - - - +
547r LEU* 3.5 19.5 + - + +
548r VAL* 3.0 26.3 + - - +
589r THR* 5.8 3.8 - - - -
817r TRP* 4.8 13.9 - - + -
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Residues in contact with ARG 545 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544r MET* 1.3 69.2 - - - +
546r SER* 1.3 69.4 + - - +
547r LEU 3.1 1.3 - - - -
548r VAL* 2.9 17.7 + - - +
549r GLN* 2.9 14.1 + - - +
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Residues in contact with SER 546 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544r MET* 4.7 0.6 - - - +
545r ARG* 1.3 76.5 - - - +
547r LEU* 1.3 57.9 + - - +
549r GLN* 3.3 8.4 + - - +
550r GLU* 2.9 32.2 + - - +
814r THR* 4.9 7.4 - - - -
817r TRP* 3.7 30.1 - - - -
818r GLY* 4.0 9.1 - - - -
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Residues in contact with LEU 547 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542r ALA* 5.1 8.7 - - + -
544r MET* 3.5 24.3 - - + +
545r ARG 3.1 0.2 - - - -
546r SER* 1.3 80.0 - - - +
548r VAL* 1.3 56.8 + - - +
550r GLU* 3.7 3.5 + - - +
551r MET* 2.9 33.2 + - - +
817r TRP* 3.7 15.2 + - + +
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Residues in contact with VAL 548 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542r ALA* 4.8 12.2 - - + +
544r MET 3.0 12.8 + - - +
545r ARG* 2.9 12.4 + - - +
547r LEU* 1.3 72.8 - - - +
549r GLN* 1.3 67.1 + - - +
551r MET* 3.2 6.2 + - - +
552r VAL* 2.9 24.7 + - - +
568r GLU* 5.3 7.1 - - + +
587r VAL* 4.8 18.4 - - + +
588r CYS* 5.2 13.5 - - - +
589r THR* 5.5 1.6 - - - +
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Residues in contact with GLN 549 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545r ARG 2.9 11.4 + - - +
546r SER* 3.4 11.4 - - - +
548r VAL* 1.3 77.5 - - - +
550r GLU* 1.3 64.8 + - + +
552r VAL* 3.1 5.7 + - - +
553r GLY* 3.0 18.9 + - - -
568r GLU* 5.6 5.6 - - - -
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Residues in contact with GLU 550 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546r SER 2.9 16.0 + - - +
547r LEU* 4.3 3.4 - - - +
549r GLN* 1.3 77.5 - - - +
551r MET* 1.3 56.3 + - - +
553r GLY* 3.2 3.9 + - - +
554r SER* 2.9 29.5 + - - -
817r TRP 5.6 0.2 - - - +
818r GLY 5.0 4.3 - - - +
819r VAL* 5.0 17.7 - - + +
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Residues in contact with MET 551 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547r LEU 2.9 21.4 + - - +
548r VAL* 3.5 6.3 - - - +
550r GLU* 1.3 75.6 - - - +
552r VAL* 1.3 59.6 + - - +
554r SER* 4.4 2.2 - - - -
555r PHE* 2.8 35.1 + - + +
587r VAL* 5.6 5.6 - - + -
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Residues in contact with VAL 552 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548r VAL 2.9 13.2 + - - +
549r GLN* 3.6 7.4 - - - +
551r MET* 1.3 75.2 - - - +
553r GLY* 1.3 57.2 + - - +
555r PHE* 4.4 5.4 - - - -
556r GLY* 3.0 26.9 + - - -
566r VAL* 4.7 8.8 - - - +
567r ALA* 4.5 9.0 - - - +
568r GLU* 4.2 28.3 - - + +
587r VAL* 5.2 7.3 - - + +
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Residues in contact with GLY 553 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549r GLN 3.0 12.8 + - - -
550r GLU* 3.4 6.5 - - - -
551r MET 3.1 0.4 - - - -
552r VAL* 1.3 79.6 - - - +
554r SER* 1.3 59.5 + - - +
556r GLY* 4.2 0.7 - - - -
557r LYS* 3.7 15.1 + - - +
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Residues in contact with SER 554 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550r GLU 2.9 16.3 + - - -
551r MET* 4.4 2.2 - - - -
553r GLY* 1.3 70.3 - - - +
555r PHE* 1.3 62.0 + - - +
556r GLY 3.2 1.6 - - - -
557r LYS* 3.2 8.0 + - - +
558r ARG* 2.9 30.2 + - - +
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Residues in contact with PHE 555 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551r MET 2.8 24.5 + - - +
552r VAL* 4.1 5.6 - - - +
554r SER* 1.3 72.0 - - - +
556r GLY* 1.3 58.8 + - - +
558r ARG* 4.4 5.2 - - - -
559r LEU* 2.9 35.7 + - + +
566r VAL* 4.9 13.1 - - + +
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Residues in contact with GLY 556 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552r VAL 3.0 19.0 + - - -
553r GLY 4.2 1.3 - - - -
554r SER 3.2 0.2 - - - -
555r PHE* 1.3 76.0 - - - +
557r LYS* 1.3 62.5 + - - +
559r LEU* 3.9 0.6 - - - -
560r ALA* 3.0 28.4 + - - +
564r ILE 5.3 4.9 - - - +
566r VAL* 5.0 12.5 - - - +
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Residues in contact with LYS 557 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553r GLY 3.7 11.3 + - - +
554r SER* 3.2 10.9 + - - +
556r GLY* 1.3 75.7 - - - +
558r ARG* 1.3 65.2 + - - +
560r ALA* 3.4 15.1 - - - +
561r THR 4.6 0.7 + - - -
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Residues in contact with ARG 558 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474r GLY* 3.8 35.1 - - - +
554r SER 2.9 16.1 + - - +
555r PHE* 3.9 6.7 - - - +
557r LYS* 1.3 80.4 - - - +
559r LEU* 1.3 63.8 + - - +
560r ALA 3.1 1.3 + - - -
561r THR* 3.8 7.6 + - - -
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Residues in contact with LEU 559 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474r GLY* 5.8 0.9 - - - -
555r PHE* 2.9 20.7 + - + +
556r GLY* 3.9 0.9 - - - +
558r ARG* 1.3 69.6 - - + +
560r ALA* 1.3 57.9 + - - +
561r THR 3.1 3.6 - - - -
562r TYR* 2.9 30.1 + - + +
563r GLY 3.4 2.9 + - - -
564r ILE* 3.9 19.8 + - + +
566r VAL* 6.1 3.6 - - + -
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Residues in contact with ALA 560 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556r GLY 3.0 19.9 + - - +
557r LYS* 3.4 13.0 - - - +
558r ARG 3.1 1.8 - - - -
559r LEU* 1.3 76.9 - - - +
561r THR* 1.3 55.7 + - - +
562r TYR 3.0 0.4 - - - -
563r GLY* 2.7 27.0 + - - +
564r ILE 4.9 3.4 - - - +
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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