Contacts of the helix formed by residues 553 - 568 (chain M) 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 VAL 553 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517M THR* 4.1 26.0 - - - -
520M ILE* 5.0 6.5 - - + -
544M GLY* 3.8 21.8 - - - +
547M LEU* 4.1 6.1 - - + -
548M PHE* 4.7 6.9 + - + +
550M TRP 4.3 0.6 + - - -
552M ASN* 1.3 78.1 - - - +
554M SER* 1.3 59.4 + - - +
555M ASP 3.3 0.7 - - - -
556M ILE* 3.4 10.7 + - + +
557M TRP* 2.9 25.1 + - - +
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Residues in contact with SER 554 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544M GLY 3.9 11.4 + - - -
545M ILE* 5.1 6.5 - - - -
548M PHE 4.9 1.6 - - - -
550M TRP 3.6 19.9 + - - -
551M PRO* 3.7 7.9 - - - -
552M ASN 3.4 1.2 - - - +
553M VAL* 1.3 78.1 - - - +
555M ASP* 1.3 59.3 + - - +
556M ILE 3.4 0.2 - - - -
557M TRP* 3.3 11.5 + - - +
558M SER* 2.9 26.2 + - - -
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Residues in contact with ASP 555 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551M PRO* 3.6 33.0 - - + +
552M ASN 4.4 4.0 - - - +
553M VAL 3.3 0.4 - - - -
554M SER* 1.3 77.0 - - - +
556M ILE* 1.3 59.4 + - - +
558M SER* 3.0 9.5 + - - +
559M THR* 2.9 27.0 + - - -
590M LYS* 6.2 2.5 - - + -
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Residues in contact with ILE 556 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520M ILE* 6.3 2.9 - - + -
521M VAL* 5.5 13.9 - - + +
552M ASN 4.4 3.8 + - - +
553M VAL* 3.4 14.8 + - - +
554M SER 3.4 0.2 - - - -
555M ASP* 1.3 78.6 - - - +
557M TRP* 1.3 57.3 + - - +
559M THR* 3.9 7.4 - - - +
560M TYR* 2.9 31.2 + - - +
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Residues in contact with TRP 557 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540M ALA* 4.4 7.6 - - - +
541M TYR* 4.3 29.6 - - + +
544M GLY* 4.6 5.8 - - - -
553M VAL 2.9 15.7 + - - +
554M SER* 3.5 14.8 - - - +
555M ASP 3.2 0.2 - - - -
556M ILE* 1.3 76.3 - - - +
558M SER* 1.3 57.6 + - - +
560M TYR* 3.8 4.7 - - - +
561M LEU* 2.9 27.2 + - - +
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Residues in contact with SER 558 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554M SER 2.9 13.7 + - - -
555M ASP* 3.0 12.3 + - - -
557M TRP* 1.3 77.1 - - - +
559M THR* 1.3 59.5 + - - +
561M LEU* 3.1 7.3 + - - +
562M THR* 2.9 28.8 + - - -
584M LEU* 6.0 6.7 - - - -
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Residues in contact with THR 559 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555M ASP 2.9 14.9 + - - -
556M ILE* 3.9 7.4 - - - -
558M SER* 1.3 77.0 - - - +
560M TYR* 1.3 57.3 + - - +
562M THR* 3.2 5.8 + - - -
563M LYS* 2.9 30.8 + - - +
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Residues in contact with TYR 560 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524M TYR* 5.8 6.3 - - + -
537M SER* 5.1 2.0 - - - -
540M ALA* 5.6 10.3 - - + -
556M ILE 2.9 19.0 + - - +
557M TRP* 3.8 5.2 - - - +
559M THR* 1.3 75.7 - - - +
561M LEU* 1.3 51.2 + - - +
563M LYS* 4.6 4.0 - - - -
564M PHE* 2.7 42.0 + - + +
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Residues in contact with LEU 561 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M SER* 6.2 0.7 - - - -
541M TYR* 5.9 5.2 - - + -
557M TRP 2.9 21.6 + - - +
558M SER* 3.4 10.1 - - - +
559M THR 3.1 0.4 - - - -
560M TYR* 1.3 76.7 - - - +
562M THR* 1.3 52.8 + - - +
564M PHE* 4.5 2.0 - - - +
565M ILE* 2.7 36.6 + - - +
580M PHE* 5.7 13.5 - - + +
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Residues in contact with THR 562 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558M SER 2.9 15.8 + - - -
559M THR* 3.2 5.4 + - - -
561M LEU* 1.3 75.5 - - - +
563M LYS* 1.3 60.8 + - - +
565M ILE* 3.2 5.5 + - - +
566M ALA* 2.9 29.6 + - - +
580M PHE* 6.5 1.1 - - - -
598M LEU* 5.7 8.7 - - - -
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Residues in contact with LYS 563 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559M THR 2.9 17.6 + - - +
560M TYR* 4.6 3.8 - - - +
562M THR* 1.3 76.2 - - - +
564M PHE* 1.3 59.1 + - - +
566M ALA* 3.3 6.0 + - - +
567M ARG* 2.9 32.9 + - - +
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Residues in contact with PHE 564 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537M SER* 3.7 29.8 - - - -
560M TYR* 2.7 24.4 + - + +
561M LEU* 4.5 2.0 - - - +
563M LYS* 1.3 74.4 - - - +
565M ILE* 1.3 60.1 + - - +
567M ARG* 3.9 2.9 - - - +
568M TYR* 2.9 37.2 + - + +
569M GLY 3.3 1.4 + - - -
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Residues in contact with ILE 565 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561M LEU 2.7 24.1 + - - +
562M THR* 3.2 8.2 + - - +
564M PHE* 1.3 78.1 - - - +
566M ALA* 1.3 57.2 + - - +
569M GLY* 3.5 6.6 + - - +
570M GLY 3.0 32.6 + - - +
576M ALA* 3.7 29.8 - - + +
580M PHE* 6.5 0.7 - - + -
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Residues in contact with ALA 566 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562M THR 2.9 15.6 + - - +
563M LYS* 3.8 5.6 - - - +
565M ILE* 1.3 79.7 - - - +
567M ARG* 1.3 60.5 + - + +
568M TYR 3.7 0.3 + - - -
570M GLY* 4.1 17.5 + - - -
571M ARG* 4.1 10.3 + - + +
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Residues in contact with ARG 567 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563M LYS 2.9 17.3 + - - +
564M PHE* 4.8 1.8 - - - +
566M ALA* 1.3 75.9 - - + +
568M TYR* 1.3 59.6 + - - +
570M GLY* 5.8 0.2 - - - -
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Residues in contact with TYR 568 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532M LYS 5.8 1.3 - - - +
533M TYR* 4.5 9.0 - - - +
534M PHE* 4.4 26.9 - - + +
537M SER* 5.7 0.4 - - - -
564M PHE* 2.9 20.6 + - + +
566M ALA 3.4 0.6 - - - -
567M ARG* 1.3 80.3 - - - +
569M GLY* 1.3 58.7 + - - +
570M GLY* 3.0 10.2 + - - -
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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