Contacts of the helix formed by residues 654 - 665 (chain B) in PDB entry 1EGI
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 654 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653B LYS* 1.3 74.0 - - - +
655B TRP* 1.3 56.7 + - - +
656B PHE* 3.5 9.0 + - - +
657B GLU* 2.9 44.1 + - - +
658B SER* 2.6 32.9 + - - -
696B TRP* 3.2 6.5 - - - -
751B CYS 3.6 11.0 - - - -
752B GLU* 3.4 22.9 - - - +
753B HIS 3.2 6.7 - - - -
754B LEU* 3.4 12.6 - - + -
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Residues in contact with TRP 655 (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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654B THR* 1.3 74.1 - - - +
656B PHE* 1.3 95.9 + + - +
658B SER* 3.2 2.3 + - - -
659B ARG* 2.7 68.7 + - + +
669B LEU* 3.3 17.0 - - + +
696B TRP* 3.2 29.0 - + + +
697B LEU 2.7 29.6 + - - -
698B GLY* 3.4 21.8 - - - -
699B LEU 3.5 6.8 + - - -
700B THR* 3.6 23.3 - - + -
732B VAL* 5.3 0.7 - - + -
735B CYS* 3.3 38.1 - - + -
751B CYS* 3.3 14.4 + - + +
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Residues in contact with PHE 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B THR* 3.3 7.3 + - - +
655B TRP* 1.3 103.2 - + - +
657B GLU* 1.3 58.2 + - + +
659B ARG* 3.1 12.9 + - - +
660B ASP* 2.8 38.6 + - - +
732B VAL* 3.5 40.6 - - + -
751B CYS* 4.0 23.1 - - + -
752B GLU* 6.2 1.8 - - + -
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Residues in contact with GLU 657 (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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652B LYS 4.8 0.3 - - - +
653B LYS* 3.4 27.0 + - + +
654B THR* 2.9 49.0 + - + +
656B PHE* 1.3 76.3 - - + +
658B SER* 1.3 57.9 + - - +
660B ASP* 3.1 12.9 + - - +
661B PHE* 2.9 29.1 + - - +
754B LEU* 4.2 3.5 - - - +
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Residues in contact with SER 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B LYS* 3.4 16.4 - - - +
654B THR 2.6 27.2 + - - -
655B TRP 3.4 4.9 - - - -
657B GLU* 1.3 72.2 - - - +
659B ARG* 1.3 64.3 + - - +
661B PHE* 3.2 8.3 + - - +
662B CYS* 3.0 27.0 + - - -
669B LEU* 3.9 10.5 - - - -
696B TRP* 3.3 17.0 - - - -
757B TRP* 3.6 28.6 - - - +
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Residues in contact with ARG 659 (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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655B TRP* 2.7 49.6 + - + +
656B PHE* 3.3 18.7 - - - +
658B SER* 1.3 73.8 - - - +
660B ASP* 1.3 65.7 + - - +
662B CYS* 3.3 2.5 + - - +
663B ARG* 2.5 75.7 + - + +
668B ASP* 4.1 7.4 + - - +
669B LEU* 3.7 19.2 - - + +
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Residues in contact with ASP 660 (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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656B PHE* 2.8 29.1 + - - +
657B GLU* 3.4 11.8 - - - +
659B ARG* 1.3 74.8 - - - +
661B PHE* 1.3 59.1 + - - +
663B ARG* 4.0 5.5 - - - +
664B ALA* 2.9 32.7 + - - +
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Residues in contact with PHE 661 (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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645B TYR* 3.3 44.2 - + - -
647B LYS* 4.6 15.0 - - - -
653B LYS* 3.4 25.1 - - - +
657B GLU 2.9 12.7 + - - +
658B SER* 3.4 11.0 - - - +
660B ASP* 1.3 79.1 - - - +
662B CYS* 1.3 62.1 + - - +
664B ALA* 3.3 16.9 - - + +
665B LEU* 3.4 32.3 + - + +
757B TRP* 3.1 31.6 - + - -
759B CYS* 3.9 2.9 - - - -
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Residues in contact with CYS 662 (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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658B SER 3.0 20.3 + - - +
659B ARG 3.9 1.3 - - - +
661B PHE* 1.3 74.8 - - - +
663B ARG* 1.3 63.5 + - - +
665B LEU* 3.1 12.5 + - - +
667B GLY* 2.9 23.5 + - - -
668B ASP* 3.4 25.8 - - - +
669B LEU* 3.7 6.3 - - - +
757B TRP* 3.8 10.5 - - - -
758B ILE 3.9 3.8 - - - -
759B CYS* 2.0 55.6 - - - -
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Residues in contact with ARG 663 (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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659B ARG* 2.5 77.8 + - - +
660B ASP* 4.1 4.9 - - - +
662B CYS* 1.3 73.7 - - - +
664B ALA* 1.3 58.1 + - - +
666B GLY* 2.8 24.9 + - - -
667B GLY 3.1 17.3 + - - +
668B ASP* 3.3 35.0 + - - +
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Residues in contact with ALA 664 (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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660B ASP 2.9 19.8 + - - +
661B PHE* 3.3 10.3 - - + +
662B CYS 3.2 0.2 - - - -
663B ARG* 1.3 78.1 - - - +
665B LEU* 1.3 61.4 + - + +
666B GLY* 3.3 0.9 + - - -
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Residues in contact with LEU 665 (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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632B TRP* 4.1 11.7 - - + -
645B TYR* 3.4 25.6 - - - +
661B PHE* 3.4 38.4 - - + +
662B CYS* 3.4 6.3 - - - +
663B ARG 3.1 0.8 - - - -
664B ALA* 1.3 77.8 - - + +
666B GLY* 1.3 57.6 + - - +
667B GLY 3.3 2.0 - - - +
759B CYS* 4.0 14.1 - - + -
761B ILE* 4.0 9.6 - - + +
766B THR 4.2 1.6 - - - +
767B PRO* 3.3 42.4 - - + +
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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