Contacts of the helix formed by residues 617 - 632 (chain B) in PDB entry 4PQP
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 TYR 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587B PRO 4.7 1.2 + - - -
589B PHE* 3.9 16.3 - + - -
615B ARG 3.9 1.2 + - - -
616B ARG* 1.3 72.2 - - - +
618B LEU* 1.3 79.4 + - + +
620B PHE* 3.2 18.9 + - - +
621B TYR* 3.6 23.2 + + - -
641B SER 4.2 1.6 + - - -
642B LYS* 3.5 20.0 - - + -
643B ARG* 2.8 33.6 + - - +
648B LYS* 4.2 26.7 - - + -
652B PHE* 3.8 22.0 - + - -
653B LEU* 4.1 34.4 - - + +
656B LYS* 4.9 4.5 - - + -
660B PHE* 3.7 29.6 - + - -
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Residues in contact with LEU 618 (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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616B ARG* 4.4 21.8 - - + +
617B TYR* 1.3 90.3 - - + +
619B GLU* 1.3 64.1 - - + +
621B TYR* 2.9 20.6 + - - +
622B VAL* 3.1 14.8 + - + +
642B LYS* 5.0 15.5 - - - +
648B LYS* 4.6 18.8 - - + +
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Residues in contact with GLU 619 (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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614B TYR 3.9 3.5 - - - +
615B ARG* 3.0 37.7 + - + -
616B ARG* 2.7 74.8 + - + +
618B LEU* 1.3 77.2 - - + +
620B PHE* 1.3 60.9 + - - +
622B VAL* 3.1 14.0 - - + +
623B LEU* 3.1 22.5 + - - +
682B PHE* 3.6 15.1 - - + -
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Residues in contact with PHE 620 (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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569B ILE* 4.2 10.8 - - + -
589B PHE* 3.4 25.1 - + + -
591B ILE* 4.1 13.9 - - + -
615B ARG* 3.7 18.4 - - + -
616B ARG 3.5 12.1 - - - -
617B TYR 3.2 10.4 + - - +
618B LEU 3.1 0.8 - - - -
619B GLU* 1.3 78.1 - - - +
621B TYR* 1.3 58.2 + - + +
623B LEU* 3.0 6.0 + - - +
624B GLU 2.9 24.6 + - - -
639B LEU* 3.4 24.7 - - + +
660B PHE* 3.4 42.2 - + + -
663B TYR* 4.5 9.8 - + - -
664B LEU* 3.9 23.3 - - + -
682B PHE* 3.9 20.9 - + - -
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Residues in contact with TYR 621 (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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617B TYR* 3.6 41.5 + + - -
618B LEU* 2.9 9.8 + - - +
620B PHE* 1.3 74.3 - - + +
622B VAL* 1.3 60.0 + - - +
624B GLU* 3.4 10.7 + - - +
625B SER* 3.0 28.1 + - - -
639B LEU* 3.7 24.9 - - + -
640B PRO* 2.5 40.6 + - - +
641B SER 3.8 1.0 + - - -
642B LYS* 3.5 47.0 - - + +
660B PHE* 3.9 16.4 - + - -
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Residues in contact with VAL 622 (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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618B LEU* 3.1 13.6 + - + +
619B GLU* 3.1 27.1 - - + +
621B TYR* 1.3 73.0 - - - +
623B LEU* 1.3 66.7 + - - +
625B SER* 3.5 6.2 - - - -
626B LYS* 2.9 49.8 + - + +
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Residues in contact with LEU 623 (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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619B GLU 3.1 13.5 + - - +
620B PHE* 3.0 9.3 + - + +
622B VAL* 1.3 79.6 - - - +
624B GLU* 1.3 58.3 + - - +
626B LYS* 3.8 3.5 - - - +
627B LEU* 2.9 54.2 + - + +
663B TYR* 4.4 12.6 - - + +
664B LEU* 4.2 11.0 - - + -
667B LEU* 4.5 1.6 - - + -
678B LEU* 3.9 30.7 - - + +
679B LEU* 4.2 14.1 - - + -
682B PHE* 3.7 43.7 - - + -
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Residues in contact with GLU 624 (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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620B PHE 2.9 14.3 + - - +
621B TYR* 3.8 13.8 - - - +
622B VAL 3.2 0.2 - - - -
623B LEU* 1.3 76.6 - - - +
625B SER* 1.3 53.7 - - - +
627B LEU* 4.0 2.4 - - - +
628B THR* 2.2 48.5 + - + +
637B ALA 4.4 1.0 - - - +
638B GLN* 3.6 17.4 - - - +
639B LEU* 3.0 49.6 + - + +
663B TYR* 3.2 24.4 - - + +
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Residues in contact with SER 625 (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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621B TYR 3.0 18.6 + - - -
622B VAL* 3.5 9.2 - - - -
624B GLU* 1.3 78.1 - - - +
626B LYS* 1.3 64.8 + - - +
628B THR* 2.5 18.7 + - - -
629B GLU* 2.9 16.7 + - - +
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Residues in contact with LYS 626 (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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622B VAL* 2.9 42.5 + - + +
623B LEU* 4.0 2.7 - - - +
625B SER* 1.3 75.8 - - - +
627B LEU* 1.3 63.0 + - - +
629B GLU* 2.9 19.6 + - - +
630B PHE* 2.9 35.6 - - + -
678B LEU* 3.5 33.3 - - + +
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Residues in contact with LEU 627 (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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623B LEU* 2.9 37.4 + - + +
624B GLU* 4.0 4.0 - - - +
626B LYS* 1.3 76.3 - - - +
628B THR* 1.3 59.8 + - + +
630B PHE 3.1 1.4 + - - -
631B HIS* 2.8 49.5 + - + +
663B TYR* 4.6 3.8 - - - +
667B LEU* 3.8 34.3 - - + -
673B LEU* 4.2 15.9 - - + -
676B SER* 3.3 27.4 - - - +
678B LEU* 3.8 14.4 - - + -
679B LEU* 4.5 8.1 - - + +
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Residues in contact with THR 628 (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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624B GLU* 2.2 43.9 + - + +
625B SER* 2.5 16.5 + - - -
627B LEU* 1.3 74.9 - - + +
629B GLU* 1.3 60.4 + - - +
632B GLY* 2.9 40.7 + - - +
633B ALA* 4.1 15.9 - - + -
634B PHE 5.3 1.1 - - - +
638B GLN* 6.1 1.6 - - - +
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Residues in contact with GLU 629 (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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625B SER* 2.9 16.0 + - - +
626B LYS* 2.9 21.2 + - - +
628B THR* 1.3 78.0 - - - +
630B PHE* 1.3 90.8 + - + +
632B GLY 5.0 0.3 + - - -
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Residues in contact with PHE 630 (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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626B LYS* 2.9 43.3 + - + -
629B GLU* 1.3 111.8 - - + +
631B HIS* 1.3 83.5 + - + +
632B GLY 3.9 0.4 - - - -
678B LEU* 3.8 15.7 - - + -
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Residues in contact with HIS 631 (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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627B LEU* 2.8 28.9 + - + +
629B GLU 3.5 0.2 - - - -
630B PHE* 1.3 98.3 + - + +
632B GLY* 1.3 58.4 + - - +
634B PHE* 4.2 18.0 - - + -
672B GLU* 3.8 30.5 + - + +
673B LEU* 3.7 26.2 - - + -
675B ASN 5.8 0.2 - - - -
676B SER* 3.4 23.3 + - - -
678B LEU* 5.3 1.7 - - + +
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Residues in contact with GLY 632 (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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628B THR* 2.9 36.7 + - - +
629B GLU 4.9 0.2 - - - -
630B PHE 3.9 0.2 - - - -
631B HIS* 1.3 80.6 - - - +
633B ALA* 1.3 62.6 + - - +
634B PHE* 4.1 3.1 - - - -
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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