Contacts of the helix formed by residues 657 - 664 (chain D) in PDB entry 5ED1
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 VAL 657 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633D TYR* 3.7 2.2 - - - -
656D ASN* 1.3 94.8 - - + +
658D TYR* 1.3 67.6 + - - +
659D HIS* 3.6 14.4 - - + +
660D GLU* 3.1 27.9 + - + +
661D SER* 3.1 20.4 + - - -
695D ASP 4.0 7.9 - - - +
696D GLN* 4.3 14.6 - - + +
697D PHE 3.3 12.6 - - - +
698D SER* 4.0 4.9 - - - +
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Residues in contact with TYR 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ARG* 5.3 0.2 + - - -
532D LEU* 3.5 25.1 - - + +
629D LYS* 3.7 35.5 + - + +
632D LEU* 5.2 4.2 - - - +
633D TYR* 3.5 32.5 + + + -
657D VAL* 1.3 71.0 - - - +
659D HIS* 1.3 62.9 + - - +
661D SER* 3.1 6.6 + - - -
662D LYS* 3.0 39.0 + - - +
695D ASP* 3.3 38.4 - - - +
697D PHE* 3.0 33.9 + + + +
801D IHP 2.6 35.2 + - - -
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Residues in contact with HIS 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D VAL* 3.3 5.7 - - + -
658D TYR* 1.3 78.4 - - - +
660D GLU* 1.3 75.1 + - - +
662D LYS* 3.0 13.4 + - + +
663D LEU* 2.9 53.4 + - + +
692D THR* 5.4 17.3 - - + +
695D ASP* 3.1 40.6 + - + +
696D GLN* 4.9 8.4 + - - +
801D IHP 5.8 2.0 - - - -
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Residues in contact with GLU 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652D ILE* 4.5 9.3 - - + +
656D ASN 5.8 1.8 - - - +
657D VAL* 3.1 33.1 + - + +
659D HIS* 1.3 89.7 + - - +
661D SER* 1.3 62.1 + - - +
663D LEU* 3.2 27.8 + - - +
664D ALA* 3.2 12.0 + - - +
696D GLN* 5.6 1.4 - - - +
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Residues in contact with SER 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D LEU* 3.8 17.3 - - - -
535D ILE* 3.7 12.6 - - - +
633D TYR* 2.7 30.8 + - - -
636D TRP* 4.7 7.9 - - - -
652D ILE* 4.6 10.0 - - - +
655D PRO* 3.7 20.1 - - - +
657D VAL 3.1 5.4 + - - -
658D TYR 3.1 10.6 + - - -
660D GLU* 1.3 76.5 - - - +
662D LYS* 1.3 62.0 + - - +
664D ALA* 3.2 17.2 + - - +
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Residues in contact with LYS 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D SER* 3.2 22.5 - - - +
532D LEU* 4.0 17.3 - - + -
629D LYS* 3.7 1.6 - - - +
658D TYR* 3.0 34.7 + - + +
659D HIS* 3.0 14.8 + - + +
661D SER* 1.3 77.3 - - - +
663D LEU* 1.3 60.9 + - + +
665D ALA* 3.1 16.3 + - - +
669D GLN* 3.0 20.6 + - - +
695D ASP* 3.5 19.2 + - - +
801D IHP 2.4 79.7 + - - +
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Residues in contact with LEU 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D HIS* 2.9 48.1 + - + +
660D GLU* 3.2 25.3 + - - +
662D LYS* 1.3 71.4 - - + +
664D ALA* 1.3 65.0 + - - +
665D ALA 3.0 4.5 + - - +
666D LYS* 3.8 13.2 + - - +
669D GLN* 4.0 28.6 - - + +
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Residues in contact with ALA 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D ILE* 4.4 4.5 - - + -
650D SER* 2.5 29.9 + - - +
651D LYS 4.9 1.6 - - - -
652D ILE* 3.6 41.5 - - + +
660D GLU 3.2 10.1 + - - +
661D SER 3.4 12.3 - - - +
662D LYS 3.2 0.8 - - - -
663D LEU* 1.3 75.7 - - - +
665D ALA* 1.3 54.4 + - - +
666D LYS* 2.8 9.0 + - - +
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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
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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