Contacts of the helix formed by residues 667 - 671 (chain B) in PDB entry 5FLM
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 667 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A PHE* 5.4 2.5 - - - -
387B HIS* 4.8 4.4 - - - -
388B TYR* 3.3 21.2 + - + +
389B GLY* 3.0 26.1 - - - -
392B ARG* 5.7 0.3 + - - -
504B THR* 3.9 22.4 - - - +
508B MET* 3.4 28.9 - - + +
621B ILE* 4.5 9.2 + - + +
666B ASP* 1.3 74.7 - - - +
668B LEU* 1.3 60.2 + - - +
670B GLU* 2.7 38.2 + - - +
671B GLU* 3.7 4.2 + - - +
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Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B HIS* 4.2 14.1 - - + -
389B GLY* 3.2 37.0 - - - +
390B ASN* 5.1 3.6 - - - +
392B ARG* 4.5 12.1 - - - +
604B ILE* 3.4 42.9 - - + +
613B ARG* 5.1 10.3 - - - +
615B TYR* 4.0 21.8 - - + +
620B ARG* 6.3 0.9 - - - -
666B ASP* 4.7 10.1 - - - +
667B THR* 1.3 80.0 + - - +
669B GLU* 1.3 59.8 + - - +
671B GLU* 3.9 22.8 - - - +
672B THR* 4.7 0.9 + - - +
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Residues in contact with GLU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET* 5.2 2.6 - - - +
588B ARG* 5.9 1.0 - - - -
591B ARG* 3.5 25.2 + - - -
602B SER* 3.7 13.9 - - - -
603B MET 3.2 26.6 + - - +
604B ILE* 3.9 11.9 - - + -
663B GLU* 4.8 0.2 - - - +
664B TYR 4.4 0.2 - - - +
665B ILE* 4.0 27.8 - - + +
666B ASP* 3.1 25.9 + - - +
667B THR 3.1 1.0 - - - -
668B LEU* 1.3 75.6 - - - +
670B GLU* 1.3 59.3 + - - +
671B GLU 3.0 2.0 - - - -
672B THR* 2.5 39.7 + - - +
673B VAL* 3.7 5.2 + - + +
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Residues in contact with GLU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A PHE* 4.1 22.2 - - + -
805A ARG* 2.7 29.3 + - - -
808A PRO* 4.2 16.1 - - + +
504B THR* 4.9 5.0 - - - +
506B TRP* 4.3 9.6 - - - +
508B MET* 3.2 20.0 - - - +
623B ARG* 3.2 38.1 + - - +
625B LEU* 5.2 2.7 - - + +
665B ILE* 3.8 12.4 - - + +
666B ASP 3.1 15.8 + - - +
667B THR* 2.7 20.8 + - - +
669B GLU* 1.3 71.3 - - - +
671B GLU* 1.3 49.2 + - - +
672B THR 3.1 0.2 - - - -
673B VAL* 3.1 21.9 - - + +
675B LEU* 5.5 0.7 - - + -
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Residues in contact with GLU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A PHE* 4.2 27.0 - - + -
803A LYS* 3.1 47.1 + - + +
805A ARG* 3.4 17.6 + - - +
812A LYS* 4.1 18.9 + - - -
387B HIS* 2.3 44.1 + - - +
667B THR 3.7 4.0 + - - +
668B LEU* 3.9 18.1 - - - +
669B GLU 3.0 1.0 - - - -
670B GLU* 1.3 78.3 - - - +
672B THR* 1.3 59.3 + - + +
673B VAL 3.4 0.4 - - - -
77I THR* 4.2 1.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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