Contacts of the helix formed by residues 611 - 621 (chain B) in PDB entry 1PG4
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 MET 611 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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603B PRO* 3.1 13.3 + - - +
605B THR* 3.5 28.0 - - + +
609B LYS 4.0 2.0 - - - +
610B ILE* 1.3 77.1 - - - +
612B ARG* 1.3 60.7 + - - +
613B ARG* 3.6 6.5 - - + +
614B ILE* 3.4 31.6 - - + +
615B LEU* 3.5 13.7 - - - +
628B ASP* 3.9 16.8 - - + -
631B THR* 3.4 32.5 - - + +
632B LEU* 3.6 17.5 - - + -
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Residues in contact with ARG 612 (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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518B ASP* 4.5 20.9 + - - +
529B THR* 3.6 11.8 - - - +
530B ALA* 5.3 5.1 - - - +
533B GLU* 2.9 37.7 + - - -
545B ALA 4.8 1.4 + - - -
546B ALA* 4.1 10.3 - - - +
547B VAL 3.8 21.5 - - - +
548B VAL* 4.2 6.6 - - + +
610B ILE* 3.8 26.8 + - - +
611B MET* 1.3 71.7 - - - +
613B ARG* 1.3 57.4 + - - +
614B ILE 3.2 2.5 - - - -
615B LEU* 2.9 11.3 + - + +
616B ARG* 2.7 52.4 + - - +
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Residues in contact with ARG 613 (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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611B MET* 3.6 6.0 - - + -
612B ARG* 1.3 77.6 - - - +
614B ILE* 1.3 66.0 + - + +
616B ARG* 3.3 21.5 + - - +
617B LYS* 3.0 43.3 + - + +
628B ASP* 5.5 14.0 - - + +
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Residues in contact with ILE 614 (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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603B PRO* 3.2 34.8 - - + -
611B MET* 3.4 19.3 - - + +
613B ARG* 1.3 77.8 - - + +
615B LEU* 1.3 69.3 + - + +
617B LYS* 3.4 10.8 + - - +
618B ILE* 3.0 37.8 + - + +
627B GLY 5.2 4.9 - - - +
628B ASP* 4.3 29.6 - - + +
629B THR* 5.0 4.7 - - - +
632B LEU* 3.6 27.4 - - + -
638B VAL* 4.8 9.9 - - + -
641B LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 615 (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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546B ALA* 3.4 33.7 - - + -
548B VAL* 4.0 6.5 - - + -
562B TYR* 2.6 52.2 + - + +
602B LEU* 4.5 2.7 - - + -
603B PRO* 3.5 32.3 - - + +
610B ILE* 6.0 1.6 - - + -
611B MET 3.5 19.3 - - - +
612B ARG* 2.9 14.6 + - + +
614B ILE* 1.3 78.8 - - - +
616B ARG* 1.3 62.7 + - - +
618B ILE* 4.6 1.1 - - - -
619B ALA* 3.0 11.1 + - - +
641B LEU* 3.6 20.2 - - + -
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Residues in contact with ARG 616 (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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517B ASP 5.7 1.8 + - - -
518B ASP* 4.2 15.2 + - - +
520B LEU* 6.2 1.0 - - - +
548B VAL* 4.0 21.4 - - + +
549B GLY 3.9 22.2 + - - +
550B ILE* 4.9 1.2 - - - +
557B GLN* 5.8 4.2 - - - +
612B ARG* 2.7 41.6 + - - +
613B ARG* 3.5 27.1 + - - +
615B LEU* 1.3 73.5 - - - +
617B LYS* 1.3 65.4 + - + +
619B ALA* 3.3 3.3 + - - +
620B ALA* 3.1 24.8 + - + +
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Residues in contact with LYS 617 (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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613B ARG* 3.0 31.5 + - + +
614B ILE* 3.8 9.6 - - - +
616B ARG* 1.3 77.4 - - + +
618B ILE* 1.3 62.6 + - + +
620B ALA* 3.3 4.4 + - - -
621B GLY 3.1 3.8 + - - -
622B ASP* 2.9 57.7 + - + +
627B GLY* 5.5 10.2 - - - +
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Residues in contact with ILE 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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562B TYR* 3.8 9.4 - - + +
614B ILE* 3.0 28.2 + - + +
615B LEU* 3.8 4.3 - - - +
617B LYS* 1.3 75.9 - - + +
619B ALA* 1.3 63.5 + - - +
621B GLY* 3.1 12.8 + - - +
622B ASP 5.0 4.5 - - - -
638B VAL* 4.2 19.1 - - + -
641B LEU* 3.9 39.0 - - + +
642B LEU* 3.9 30.3 - - + -
645B LYS* 3.6 34.9 - - + +
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Residues in contact with ALA 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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548B VAL* 3.8 6.3 - - + -
550B ILE* 3.4 31.3 - - + +
560B TYR* 3.8 21.9 - - + -
562B TYR* 3.4 10.2 + - - +
615B LEU 3.0 18.4 + - - +
616B ARG 3.7 2.9 - - - +
618B ILE* 1.3 76.7 - - - +
620B ALA* 1.3 59.2 + - - +
645B LYS* 3.2 26.1 + - - +
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Residues in contact with ALA 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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550B ILE* 4.1 6.5 - - + +
551B PRO* 3.8 27.8 - - + +
616B ARG* 3.1 18.0 + - + +
617B LYS* 3.8 6.3 - - - +
619B ALA* 1.3 76.3 - - - +
621B GLY* 1.3 57.9 + - - +
622B ASP* 3.4 8.4 + - + +
645B LYS* 5.3 0.9 - - - -
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Residues in contact with GLY 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 LYS 3.1 3.4 + - - -
618B ILE* 3.1 12.4 + - - -
619B ALA 3.3 0.6 - - - -
620B ALA* 1.3 79.5 - - - +
622B ASP* 1.3 62.2 - - - +
645B LYS* 4.9 8.5 - - - -
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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