Contacts of the helix formed by residues 674 - 684 (chain B) in PDB entry 1FO4
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 674 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ARG* 6.0 0.2 - - - -
604B PHE* 3.6 8.3 - - - +
672B ALA* 3.2 2.1 - - - +
673B ASP* 1.3 98.9 + - + +
675B PRO* 1.3 73.9 - - - +
676B GLU* 3.7 10.5 + - - +
677B HIS* 3.1 34.4 + - + +
678B ALA* 3.1 21.1 + - - +
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Residues in contact with PRO 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ARG* 3.3 36.6 - - - +
604B PHE* 3.7 41.3 - - + -
606B ARG* 5.5 0.5 - - - +
674B THR* 1.3 86.4 - - - +
676B GLU* 1.3 72.4 + - - +
678B ALA* 3.2 4.7 + - + +
679B GLU* 3.0 25.2 + - - +
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Residues in contact with GLU 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 5.4 2.7 - - - +
32B ARG* 3.2 31.8 + - - -
269B LYS* 6.0 0.3 + - - -
674B THR* 3.3 8.7 + - - +
675B PRO* 1.3 90.3 - - - +
677B HIS* 1.3 61.5 + - + +
679B GLU* 3.4 15.1 + - - +
680B ARG* 3.0 53.1 + - - +
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Residues in contact with HIS 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 2.9 30.1 + - - -
628B VAL* 3.8 10.5 - - + +
629B PRO* 3.0 38.1 + - + +
672B ALA* 3.8 7.2 - - + +
673B ASP* 2.8 31.1 + - - +
674B THR* 3.1 21.1 + - + +
676B GLU* 1.3 80.3 - - + +
678B ALA* 1.3 58.7 + - - +
680B ARG* 3.4 19.0 + - - +
681B ALA* 3.0 31.7 + - - +
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Residues in contact with ALA 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B PHE* 3.9 19.7 - - + +
605B LEU 4.5 0.4 - - - -
606B ARG* 3.4 21.1 - - + +
670B VAL* 3.9 10.7 - - - +
672B ALA* 3.4 17.2 - - + +
674B THR 3.1 15.9 + - - +
675B PRO* 3.2 6.5 + - + +
677B HIS* 1.3 76.7 - - - +
679B GLU* 1.3 58.6 + - - +
682B ALA* 3.0 30.7 + - - +
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Residues in contact with GLU 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B LYS* 3.4 29.4 + - - +
606B ARG* 3.2 46.7 + - - +
675B PRO 3.0 16.5 + - - +
676B GLU* 3.6 14.7 - - - +
678B ALA* 1.3 76.3 - - - +
680B ARG* 1.3 62.8 + - + +
682B ALA* 3.5 1.2 + - - +
683B HIS* 3.0 28.6 + - + +
828B ASP* 3.4 10.2 - - - +
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Residues in contact with ARG 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 3.6 22.2 + - - +
232B GLU* 2.7 38.6 + - - +
233B ARG* 3.5 43.6 - - - +
628B VAL* 4.1 17.4 - - + +
629B PRO* 5.7 0.4 - - - +
676B GLU* 3.0 36.9 + - - +
677B HIS* 3.4 15.2 + - - +
679B GLU* 1.3 77.1 - - + +
681B ALA* 1.3 67.0 + - - +
683B HIS* 3.4 15.7 + - - +
684B VAL* 3.5 17.7 + - - +
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Residues in contact with ALA 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B ALA* 3.1 31.9 - - + +
628B VAL* 3.5 25.0 - - + +
631B PHE* 4.0 8.5 - - + -
670B VAL* 3.7 21.5 - - + -
677B HIS 3.0 18.2 + - - +
680B ARG* 1.3 77.7 - - - +
682B ALA* 1.3 63.0 + - - +
684B VAL* 3.2 10.4 + - - +
685B VAL* 3.4 2.5 - - - +
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Residues in contact with ALA 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B ARG* 3.5 23.1 - - + +
607B LEU 4.4 4.0 - - - +
608B VAL* 4.2 16.9 - - + +
670B VAL* 3.7 19.7 - - + +
678B ALA 3.0 20.2 + - - +
679B GLU 3.9 2.5 - - - +
681B ALA* 1.3 77.3 - - - +
683B HIS* 1.3 63.4 + - - +
685B VAL* 3.3 18.5 + - - +
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Residues in contact with HIS 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ASN* 3.1 43.6 + - + +
679B GLU* 3.0 19.2 + - + +
680B ARG* 3.6 8.1 - - - +
681B ALA 3.2 0.4 - - - -
682B ALA* 1.3 78.6 - - - +
684B VAL* 1.3 70.2 + - + +
685B VAL 3.4 3.7 + - - +
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Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B ASP 4.3 1.9 - - - +
624B GLU* 3.7 27.5 - - + +
625B ALA* 3.5 24.6 + - - +
628B VAL* 4.4 4.5 - - + -
680B ARG 3.6 11.9 - - - +
681B ALA* 3.2 14.6 - - - +
682B ALA 3.2 0.2 - - - -
683B HIS* 1.3 90.8 - - + +
685B VAL* 1.3 62.7 + - - +
686B LYS* 3.1 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