Contacts of the helix formed by residues 687 - 696 (chain E) in PDB entry 1FM6
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 HIS 687 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315D VAL* 3.6 26.4 - - + +
319D LYS* 2.5 48.1 + - + +
471D GLU* 2.8 56.1 + - + +
474D LYS 4.6 0.4 + - - -
685E GLU* 3.2 36.1 + - + +
686E ARG* 1.3 80.5 - - - +
688E LYS* 1.3 62.4 + - - +
690E LEU* 4.2 13.0 - - + -
691E HIS* 3.2 18.7 + - - -
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Residues in contact with LYS 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D GLU* 3.3 5.8 + - - +
686E ARG* 3.1 24.6 + - + +
687E HIS* 1.3 75.2 - - - +
689E ILE* 1.3 60.7 + - - +
691E HIS* 3.4 5.7 - - - +
692E ARG* 3.2 21.0 + - - +
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Residues in contact with ILE 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D HIS* 5.0 4.7 - - + -
467D PRO* 4.9 8.3 - - + -
468D LEU* 3.1 56.3 - - + +
471D GLU* 2.8 34.1 + - - +
688E LYS* 1.3 75.2 - - - +
690E LEU* 1.3 65.4 + - - +
692E ARG* 3.4 32.8 + - - +
693E LEU* 3.2 29.7 + - + +
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Residues in contact with LEU 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL* 4.0 19.1 - - + -
297D THR* 4.7 6.5 - - - +
315D VAL* 3.7 38.1 - - + +
318D LEU* 4.3 11.7 - - + -
319D LYS* 4.2 11.7 - - - +
468D LEU* 3.9 22.2 - - + -
471D GLU* 2.9 12.2 + - - +
472D ILE* 4.3 17.0 - - + -
687E HIS* 3.3 19.3 + - + +
689E ILE* 1.3 74.0 - - - +
691E HIS* 1.3 67.0 + - - +
693E LEU* 3.3 9.7 + - + +
694E LEU* 2.9 30.4 + - + +
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Residues in contact with HIS 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 3.6 41.3 - - + +
312D ASN* 4.5 8.5 + - - -
315D VAL* 3.9 17.2 - - + +
686E ARG* 3.0 45.5 + - - +
687E HIS* 3.2 16.7 + - + -
688E LYS* 3.4 10.3 - - - +
690E LEU* 1.3 78.6 - - - +
692E ARG* 1.3 63.9 + - - +
694E LEU* 2.9 10.7 + - - +
695E GLN* 2.8 30.8 + - + +
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Residues in contact with ARG 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D GLN* 4.4 7.5 + - - +
688E LYS 3.2 10.1 + - - +
689E ILE* 3.5 35.8 - - - +
691E HIS* 1.3 78.4 - - - +
693E LEU* 1.3 80.3 + - - +
695E GLN* 4.6 2.7 - - - +
696E GLU* 2.8 53.4 + - + +
697E GLY 3.3 9.6 + - - +
699E PRO* 3.5 31.7 - - - +
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Residues in contact with LEU 693 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D VAL* 4.5 5.2 - - + -
294D GLN* 3.9 23.1 - - + +
297D THR* 3.9 27.3 - - + +
298D GLU* 4.6 0.2 - - - +
301D LYS* 2.7 29.1 + - - -
468D LEU* 4.3 18.4 - - + -
689E ILE* 3.2 18.0 + - + +
690E LEU* 3.6 12.1 - - + +
692E ARG* 1.3 98.9 - - - +
694E LEU* 1.3 51.7 + - - +
697E GLY* 3.0 29.6 + - - +
698E SER* 3.8 16.8 - - - +
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Residues in contact with LEU 694 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D THR* 4.2 3.1 - - + +
301D LYS* 3.2 39.9 + - + +
306D PHE* 3.7 13.5 - - + -
307D VAL* 5.7 2.0 - - + +
311D LEU* 4.2 12.1 - - + -
314D GLN* 3.4 33.2 - - + +
315D VAL* 3.4 33.4 - - + -
318D LEU* 3.5 30.7 - - + -
690E LEU 2.9 12.7 + - - +
691E HIS* 2.9 8.8 + - - +
693E LEU* 1.3 76.0 - - - +
695E GLN* 1.3 60.8 + - - +
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Residues in contact with GLN 695 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D LYS* 5.0 0.9 + - - -
311D LEU* 4.6 22.7 - - + +
691E HIS* 2.8 19.9 + - + +
692E ARG* 3.8 3.6 - - - +
694E LEU* 1.3 82.7 - - + +
696E GLU* 1.3 70.8 + - + +
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Residues in contact with GLU 696 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D LYS* 4.6 2.0 - - - -
692E ARG* 2.8 35.1 + - + +
695E GLN* 1.3 87.0 - - + +
697E GLY* 1.3 62.1 + - - +
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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