Contacts of the helix formed by residues 654 - 665 (chain A) in PDB entry 5E2Q
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 SER 654 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591A PRO* 6.0 2.2 - - - -
649A ASP* 3.2 35.3 + - - -
650A ALA 2.9 21.2 + - - -
651A PRO* 4.4 4.0 - - - +
652A PRO 3.9 7.1 + - - -
653A GLU* 1.3 76.7 - - - +
655A PHE* 1.3 60.6 + - - +
657A THR* 3.2 10.5 + - - -
658A LEU* 2.9 23.6 + - - +
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Residues in contact with PHE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 4.8 4.0 - - + -
554A LEU* 3.5 24.1 - - + +
573A PHE* 3.6 25.4 - + - -
576A LEU* 4.1 15.3 - - + -
577A ARG* 3.6 27.1 - - - -
580A LEU* 3.7 17.0 - - + -
589A ILE* 4.7 5.2 - - + -
646A THR 5.4 0.4 - - - -
647A VAL* 4.1 14.6 - - + -
648A THR* 3.2 20.5 + - + +
650A ALA 4.8 0.2 + - - -
653A GLU* 3.6 33.7 - - + -
654A SER* 1.3 75.7 - - - +
656A LEU* 1.3 53.3 + - - +
658A LEU* 4.0 16.6 - - + -
659A ARG* 2.8 35.0 + - - +
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Residues in contact with LEU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A TYR* 4.4 5.2 - - + -
559A PRO* 4.4 26.2 - - + -
647A VAL* 3.7 23.1 - - + +
648A THR* 3.3 17.8 + - - +
649A ASP* 3.3 32.4 + - + +
655A PHE* 1.3 78.4 - - - +
657A THR* 1.3 60.9 + - - +
659A ARG* 3.6 18.3 - - - +
660A ASP* 3.8 11.6 - - - +
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Residues in contact with THR 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ASP* 2.5 34.9 + - - -
654A SER* 3.2 11.6 + - - -
656A LEU* 1.3 74.1 - - - +
658A LEU* 1.3 65.7 + - - +
659A ARG 3.2 0.2 - - - -
660A ASP* 3.3 25.9 + - - +
661A THR* 3.9 5.9 + - - -
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Residues in contact with LEU 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 3.9 13.2 - - + -
554A LEU* 4.2 6.3 - - + -
589A ILE* 3.6 28.0 - - + -
591A PRO* 4.2 23.3 - - + -
600A ASP 5.1 0.7 - - - +
601A ALA* 4.0 26.2 - - + -
653A GLU 3.3 20.4 - - - +
654A SER* 2.9 12.0 + - - +
655A PHE* 3.5 22.2 - - + +
657A THR* 1.3 77.7 - - + +
659A ARG* 1.3 59.3 + - - +
661A THR* 2.9 28.6 + - - +
662A VAL* 2.9 15.6 + - - +
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Residues in contact with ARG 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLN* 5.3 4.6 + - - -
554A LEU* 3.1 37.3 + - + +
555A GLU 4.3 8.3 + - - -
557A TYR* 2.7 38.1 + - - -
558A THR* 4.5 1.0 - - - +
559A PRO* 3.5 32.3 - - - +
560A GLU* 5.9 0.2 + - - -
565A ARG* 4.4 4.2 - - - +
647A VAL* 5.8 0.7 - - + -
655A PHE 2.8 16.5 + - - +
656A LEU* 3.6 16.2 - - - +
657A THR 3.2 0.2 - - - -
658A LEU* 1.3 77.2 - - - +
660A ASP* 1.3 64.8 + - - +
662A VAL* 3.2 3.0 + - - +
663A LEU* 3.0 56.7 + - + +
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Residues in contact with ASP 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A LEU 3.8 13.7 - - - +
657A THR* 3.5 17.0 - - - +
658A LEU 3.1 0.6 - - - -
659A ARG* 1.3 88.4 + - - +
661A THR* 1.3 57.2 + - - +
663A LEU* 3.7 9.1 + - - +
664A LEU* 3.2 26.7 + - - +
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Residues in contact with THR 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PHE* 3.8 17.6 - - + -
599A PRO* 3.3 41.7 - - - +
600A ASP* 3.6 21.1 + - - -
601A ALA* 4.7 0.7 - - + -
657A THR 4.1 6.8 + - - -
658A LEU* 2.9 19.8 + - - +
660A ASP* 1.3 77.3 - - - +
662A VAL* 1.3 64.7 + - - +
664A LEU* 3.3 5.6 + - - -
665A ARG* 3.2 26.4 + - - +
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Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PHE* 3.9 13.9 - - + -
551A LEU* 3.3 39.5 - - + +
552A LEU* 3.5 36.5 - - + +
554A LEU* 4.2 2.9 - - + -
555A GLU* 3.9 17.3 - - + +
658A LEU 2.9 20.6 + - - +
659A ARG* 3.2 11.8 + - - +
661A THR* 1.3 78.1 - - - +
663A LEU* 1.3 56.8 + - - +
665A ARG 3.7 1.4 - - - -
666A LYS* 3.1 28.3 + - + +
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 4.6 8.1 + - - +
5A GLN* 3.4 36.8 - - + +
555A GLU* 3.7 42.4 - - + +
659A ARG* 3.0 54.0 + - + +
660A ASP* 4.0 9.6 - - - +
662A VAL* 1.3 74.1 - - - +
664A LEU* 1.3 65.0 + - - +
666A LYS* 3.3 30.9 - - + +
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Residues in contact with LEU 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.2 18.6 - - + +
3A ASP 4.8 2.7 + - - +
598A ARG* 3.3 68.6 + - + +
599A PRO* 4.2 23.6 - - + +
660A ASP 3.2 19.3 + - - +
661A THR* 3.7 6.7 - - - +
662A VAL 3.3 0.4 - - - -
663A LEU* 1.3 78.2 - - - +
665A ARG* 1.3 59.0 + - + +
666A LYS 3.5 0.7 + - - +
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Residues in contact with ARG 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A THR* 3.9 28.3 + - + +
426A PHE* 4.2 14.1 - - + -
552A LEU* 6.0 0.5 - - - +
594A GLY* 4.7 4.2 - - - -
595A SER 5.4 0.4 - - - +
596A ASP* 3.6 24.6 + - - +
598A ARG* 3.6 36.8 + - - +
599A PRO 2.9 28.9 + - - +
600A ASP* 3.5 34.1 + - - +
661A THR* 3.2 20.7 + - - +
662A VAL 3.7 2.5 - - - -
664A LEU* 1.3 86.0 - - + +
666A LYS* 1.3 65.0 + - - +
667A GLU* 3.8 2.4 + - - +
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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