Contacts of the helix formed by residues 620 - 631 (chain B) in PDB entry 6PUO
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 ASP 620 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B LYS* 4.8 5.7 + - - +
618B THR 3.4 0.8 + - - -
619B MET* 1.3 92.1 - - + +
621B PRO* 1.3 73.9 - - - +
622B ILE* 3.9 17.8 + - - +
623B ARG* 3.2 35.2 + - + +
624B ASP* 3.3 2.1 - - - +
645B SER* 5.6 0.9 + - - -
646B GLN* 3.8 32.4 + - - +
647B ASP* 4.4 9.5 - - - +
711B ALA* 4.3 11.6 - - + +
712B TRP* 5.6 0.3 + - - -
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Residues in contact with PRO 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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510B LEU 4.5 1.3 - - - +
511B LYS* 4.1 42.8 - - + +
514B VAL* 3.7 35.1 - - + +
617B PHE* 5.1 3.8 - - + -
618B THR* 4.1 16.4 - - + +
619B MET 3.8 0.4 - - - -
620B ASP* 1.3 89.1 - - - +
622B ILE* 1.3 61.9 + - + +
623B ARG 3.2 0.2 - - - -
624B ASP* 2.9 31.0 + - - +
625B LEU* 3.0 12.4 + - - +
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Residues in contact with ILE 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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510B LEU* 5.0 18.6 - - + +
511B LYS* 3.9 33.9 - - + +
514B VAL* 5.8 1.3 - - + -
620B ASP* 3.2 12.0 - - - +
621B PRO* 1.3 85.8 - - + +
623B ARG* 1.3 57.9 + - - +
625B LEU* 3.4 7.7 + - + +
626B LEU* 2.9 29.0 + - + +
641B ILE* 4.1 28.4 - - + +
644B GLN* 3.5 30.7 - - + +
645B SER* 4.4 13.0 - - - +
646B GLN* 5.6 1.3 - - + +
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Residues in contact with ARG 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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576B LEU* 3.4 39.0 + - - +
577B TYR* 3.8 8.3 + - - -
618B THR* 4.4 8.9 + - - -
619B MET* 3.6 26.4 + - - +
620B ASP* 3.2 27.0 + - - +
622B ILE* 1.3 78.1 - - - +
624B ASP* 1.3 87.3 + - - +
626B LEU* 3.3 8.6 + - - +
627B ILE* 2.9 34.4 + - - +
645B SER* 5.9 2.0 + - - +
710B GLU 5.8 0.2 + - - -
711B ALA* 3.0 42.8 + - - +
712B TRP* 3.8 28.0 - - + +
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Residues in contact with ASP 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 5.4 1.3 - - + -
519B LEU* 3.9 23.8 - - + +
523B TYR* 4.1 3.6 + - - -
577B TYR* 2.4 37.8 + - - +
618B THR* 3.3 27.5 - - - +
620B ASP 3.3 3.7 - - - +
621B PRO* 2.9 18.1 + - - +
623B ARG* 1.3 101.2 + - - +
625B LEU* 1.3 60.4 + - - +
627B ILE* 3.4 4.8 + - - +
628B TRP* 3.0 28.6 + - - +
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Residues in contact with LEU 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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492B LEU* 4.3 18.6 - - + -
510B LEU* 4.4 20.2 - - + -
513B PHE* 5.1 1.6 - - + -
514B VAL* 4.1 29.4 - - + -
519B LEU* 4.8 4.0 - - + +
522B LEU* 4.1 26.9 - - + -
621B PRO 3.0 10.2 + - - +
622B ILE* 3.8 10.8 - - + +
624B ASP* 1.3 77.4 - - - +
626B LEU* 1.3 55.7 + - - +
628B TRP* 3.4 14.0 + - + +
629B ALA* 2.9 28.4 + - - +
641B ILE* 3.8 29.8 - - + +
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Residues in contact with LEU 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 ILE* 2.9 17.9 + - + +
623B ARG* 3.6 9.6 - - - +
624B ASP 3.2 0.2 - - - -
625B LEU* 1.3 77.0 - - - +
627B ILE* 1.3 57.3 + - + +
629B ALA* 3.2 2.0 + - + -
630B ILE* 2.9 38.6 + - + +
638B ALA* 4.1 32.5 - - + +
641B ILE* 4.1 19.2 - - + +
642B TRP* 4.0 31.0 - - + +
645B SER* 5.2 5.6 - - - -
651B ALA* 4.5 12.3 - - + -
655B CYS* 4.0 22.2 - - - -
682B TYR* 4.9 1.8 - - + +
712B TRP* 5.3 3.4 - - + -
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Residues in contact with ILE 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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523B TYR* 3.7 11.9 - - - +
532B PHE* 6.3 1.1 - - + -
565B LEU* 3.8 32.8 - - + -
576B LEU* 4.0 22.4 - - + -
577B TYR* 5.0 2.9 - - - +
623B ARG* 2.9 27.2 + - + +
624B ASP* 3.9 6.7 - - - +
626B LEU* 1.3 75.5 - - + +
628B TRP* 1.3 62.4 + - - +
630B ILE* 3.4 12.6 + - - +
631B VAL* 3.4 23.7 + - + +
655B CYS* 5.8 3.4 - - - -
658B ILE* 4.9 13.0 - - + -
712B TRP* 3.8 32.1 - - + -
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Residues in contact with TRP 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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492B LEU* 3.5 43.1 - - + -
493B ILE* 4.6 7.2 - - + -
519B LEU* 5.2 2.0 - - + -
522B LEU* 3.0 49.1 + - + -
523B TYR* 3.4 45.4 + + + +
525B ASN 5.0 5.4 - - - -
526B LEU* 4.3 1.2 - - - +
624B ASP 3.0 17.9 + - - +
625B LEU* 3.7 19.5 - - + +
627B ILE* 1.3 78.3 - - - +
629B ALA* 1.3 75.0 + - + +
630B ILE 3.6 0.2 + - - -
631B VAL* 3.8 4.1 - - - +
632B GLN* 3.2 51.4 + - - +
634B ARG* 4.5 4.7 - - - -
637B LEU* 4.6 8.3 - - + -
641B ILE* 5.9 1.3 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.4 + - - +
626B LEU* 3.2 5.3 + - - +
628B TRP* 1.3 89.6 - - + +
630B ILE* 1.3 66.3 + - - +
632B GLN* 4.0 2.7 + - - -
633B ASN 4.0 1.4 + - - -
634B ARG* 3.5 29.2 + - + +
637B LEU* 4.5 15.9 - - + -
638B ALA* 4.5 9.4 - - + +
641B ILE* 4.2 17.3 - - + -
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Residues in contact with ILE 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU* 2.9 25.2 + - + +
627B ILE* 3.4 5.6 + - - +
628B TRP 3.3 0.2 - - - -
629B ALA* 1.3 79.0 - - - +
631B VAL* 1.3 57.6 + - + +
633B ASN* 2.8 28.5 + - - +
634B ARG 5.4 0.4 - - - +
638B ALA* 3.7 23.1 - - + -
655B CYS* 3.7 30.5 - - + +
658B ILE* 4.4 16.4 - - + -
659B LEU* 3.8 45.3 - - + +
675B MET* 5.6 0.2 - - - +
678B LEU* 4.5 10.5 - - + +
682B TYR* 4.6 9.4 - - + +
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Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B TYR* 5.1 3.4 - - + +
526B LEU* 4.7 2.7 - - + -
530B CYS* 4.5 6.8 - - - +
532B PHE* 3.9 56.9 + - + +
565B LEU* 5.1 3.1 - - + -
568B LEU* 5.5 1.3 - - + -
627B ILE* 3.4 27.6 - - + +
628B TRP* 3.8 11.0 - - - +
630B ILE* 1.3 76.4 - - + +
632B GLN* 1.3 65.4 + - + +
633B ASN 3.3 0.8 + - - -
658B ILE* 4.4 21.1 - - + -
659B LEU* 5.5 0.2 - - - -
662B LEU* 4.2 19.8 - - + +
675B MET* 4.6 5.7 - - - +
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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