Contacts of the helix formed by residues 48 - 57 (chain 1) 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 THR 48 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2250 SER* 4.3 10.8 - - - -
2260 PHE* 3.2 38.1 - - - -
2270 GLU 4.2 10.9 + - - -
461 GLU 3.8 3.4 + - - -
471 LEU* 1.3 76.2 - - - +
491 GLU* 1.3 66.4 + - - +
501 GLY 3.3 2.7 - - - -
511 ASP* 3.6 10.6 + - - +
521 ILE* 3.4 20.3 + - - +
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Residues in contact with GLU 49 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2240 PRO* 6.2 4.2 - - + +
2260 PHE* 4.9 3.2 - - + +
481 THR* 1.3 77.5 - - - +
501 GLY* 1.3 57.4 + - - +
521 ILE* 3.4 7.4 + - - +
531 ILE* 3.0 28.1 + - - +
651 ILE* 5.3 12.6 - - + -
671 LEU* 5.7 7.9 - - + -
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Residues in contact with GLY 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2260 PHE* 4.7 15.7 - - - +
481 THR* 3.3 3.8 - - - -
491 GLU* 1.3 80.1 - - - +
511 ASP* 1.3 56.1 + - - +
531 ILE* 3.3 7.5 + - - +
541 CYS* 2.9 29.0 + - - +
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Residues in contact with ASP 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2260 PHE 6.1 0.2 - - - -
2270 GLU 5.6 4.3 - - - +
2280 LEU* 6.2 2.2 - - - -
2320 LEU* 6.2 4.7 - - + -
471 LEU* 5.1 6.7 - - + -
481 THR* 3.6 19.8 + - - +
491 GLU 3.4 0.4 - - - -
501 GLY* 1.3 73.6 - - - +
521 ILE* 1.3 61.0 + - - +
541 CYS* 3.3 7.5 + - - +
551 VAL* 2.9 30.5 + - - +
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Residues in contact with ILE 52 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 LEU* 5.7 5.1 - - + +
481 THR 3.4 11.5 + - - +
491 GLU* 3.7 10.3 - - - +
501 GLY 3.3 0.4 - - - -
511 ASP* 1.3 75.6 - - - +
531 ILE* 1.3 58.5 + - - +
551 VAL* 3.4 3.7 + - - +
561 PHE* 2.9 34.0 + - - +
801 CYS* 6.1 4.7 - - + -
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Residues in contact with ILE 53 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 GLU 3.0 17.6 + - - +
501 GLY* 3.6 7.9 - - - +
521 ILE* 1.3 76.8 - - - +
541 CYS* 1.3 56.2 + - - +
561 PHE* 5.3 1.3 - - - -
571 SER* 2.9 39.0 + - - +
621 ILE* 5.8 10.8 - - + +
5843 TRP* 5.8 3.4 - - + -
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Residues in contact with CYS 54 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501 GLY 2.9 17.0 + - - +
511 ASP* 3.3 8.2 + - - +
531 ILE* 1.3 75.7 - - - +
551 VAL* 1.3 60.0 + - - +
561 PHE 3.8 0.2 + - - -
571 SER 4.2 2.4 + - - -
581 GLN* 5.8 0.2 - - - +
5843 TRP* 4.0 10.5 - - - +
5853 ASP* 2.9 37.5 - - + +
5863 GLY* 4.9 0.9 - - - -
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Residues in contact with VAL 55 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511 ASP 2.9 17.0 + - - +
521 ILE* 4.2 3.8 - - - +
541 CYS* 1.3 77.0 - - - +
561 PHE* 1.3 60.3 + - - +
571 SER 3.6 0.2 - - - -
581 GLN* 4.6 9.8 + - - +
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Residues in contact with PHE 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521 ILE 2.9 16.4 + - - +
531 ILE* 3.7 2.2 - - - -
551 VAL* 1.3 79.4 - - - +
571 SER* 1.3 55.2 + - - +
581 GLN* 3.3 6.4 + - - -
591 TYR* 4.4 4.6 + - - +
601 GLY 3.4 10.4 - - - +
621 ILE* 5.3 7.2 + - + +
821 LEU* 5.8 7.9 - - + -
931 ALA* 6.4 1.8 - - + -
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Residues in contact with SER 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531 ILE* 2.9 21.3 + - - -
541 CYS 4.2 1.0 + - - -
551 VAL 3.6 1.0 - - - -
561 PHE* 1.3 76.4 - - - +
581 GLN* 1.3 62.8 + - - +
591 TYR 3.3 2.2 - - - -
601 GLY 3.4 21.0 + - - +
611 GLU* 4.3 10.1 - - - -
621 ILE 5.2 1.3 - - - +
5833 ARG 2.9 32.1 + - - +
5843 TRP* 3.4 21.5 - - - -
5863 GLY* 4.8 0.4 - - - -
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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