Contacts of the helix formed by residues 610 - 622 (chain B) in PDB entry 4GDF
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 610 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608B SER* 2.8 7.7 + - - -
609B LEU* 1.3 84.1 - - - +
611B VAL* 1.3 57.1 - - - +
612B TYR 3.0 2.0 - - - -
613B GLN* 2.6 36.5 + - - +
614B LYS* 2.9 12.4 + - - +
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Residues in contact with VAL 611 (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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607B PHE* 5.2 7.2 - - + -
608B SER* 2.7 47.6 + - - +
610B SER* 1.3 71.9 - - - +
612B TYR* 1.3 62.0 + - - +
614B LYS* 3.3 9.8 + - + +
615B MET* 3.2 38.4 + - + +
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Residues in contact with TYR 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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388B MET* 4.0 17.5 - - + -
391B VAL* 3.8 6.6 + - + +
392B ALA* 3.6 42.0 - - + -
395B HIS* 3.7 8.7 - - - +
581B TRP* 3.2 42.6 - + + +
582B TYR* 2.6 38.0 + + - -
607B PHE* 5.9 4.2 - - + +
608B SER 3.7 9.6 + - - +
609B LEU 5.1 2.7 - - - +
610B SER 3.0 0.6 - - - -
611B VAL* 1.3 80.6 - - - +
613B GLN* 1.3 64.3 + - + +
615B MET* 2.9 19.7 + - + +
616B LYS* 2.9 40.3 + - + +
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Residues in contact with GLN 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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609B LEU 2.7 25.3 - - - +
610B SER* 2.6 25.6 + - - +
612B TYR* 1.3 82.2 - - + +
614B LYS* 1.3 59.2 + - - +
616B LYS* 3.5 8.5 + - + +
617B PHE* 3.4 20.1 + - - +
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Residues in contact with LYS 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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610B SER* 2.9 10.8 + - - +
611B VAL* 3.6 12.8 - - + +
612B TYR 3.2 0.2 - - - -
613B GLN* 1.3 78.4 - - - +
615B MET* 1.3 60.9 + - + +
617B PHE* 3.2 35.9 - - + +
618B ASN* 3.0 33.2 + - - +
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Residues in contact with MET 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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385B GLU 5.1 3.4 - - - +
388B MET* 4.7 14.6 - - + +
389B ALA* 4.2 14.8 - - - -
392B ALA* 4.2 9.0 - - + +
607B PHE* 4.9 9.4 - - + -
611B VAL* 3.2 32.5 + - + +
612B TYR* 2.9 31.5 + - + +
614B LYS* 1.3 75.3 - - + +
616B LYS* 1.3 57.6 + - - +
617B PHE 2.8 8.1 + - - -
618B ASN* 2.6 21.7 - - - +
619B VAL* 3.1 15.8 + - - +
625B VAL* 3.7 37.7 - - + +
626B LEU* 4.7 12.1 - - - +
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Residues in contact with LYS 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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392B ALA* 4.2 13.2 - - + +
395B HIS* 2.7 51.3 + - - -
396B CYS* 3.8 16.7 - - - -
582B TYR* 3.4 15.9 + - - +
612B TYR* 2.9 25.3 + - + +
613B GLN* 3.8 9.2 - - + +
614B LYS 3.5 0.2 - - - -
615B MET* 1.3 74.6 - - - +
617B PHE* 1.3 56.1 + - - +
619B VAL* 3.4 15.8 - - - +
620B ALA* 4.2 7.4 - - - +
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Residues in contact with PHE 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 GLN 3.4 11.8 + - - +
614B LYS* 3.2 40.4 - - + +
615B MET 2.8 2.2 - - - -
616B LYS* 1.3 78.3 - - - +
618B ASN* 1.3 67.2 + - + +
619B VAL 3.0 4.0 - - - -
620B ALA* 2.7 29.6 + - - +
621B MET* 3.2 49.0 + - + +
623B ILE* 5.8 3.6 - - + -
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Residues in contact with ASN 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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614B LYS* 3.0 27.5 + - - +
615B MET* 2.6 33.1 - - - +
617B PHE* 1.3 82.9 - - + +
619B VAL* 1.3 57.9 + - - +
620B ALA 3.1 0.2 - - - -
621B MET* 3.5 12.6 - - - -
622B GLY 2.9 26.2 + - - -
623B ILE* 3.1 30.5 + - + +
624B GLY 3.5 17.8 + - - +
625B VAL* 3.4 19.8 + - - +
626B LEU 5.1 1.0 + - - -
627B ASP 5.5 2.2 + - - -
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Residues in contact with VAL 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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392B ALA* 4.4 2.9 - - + +
393B TRP* 3.5 41.1 - - + +
396B CYS* 3.4 19.3 - - - -
552B TYR* 2.8 26.4 - - - +
553B LEU* 3.7 10.8 - - + +
556B CYS* 3.6 20.1 - - - +
615B MET 3.1 19.7 - - - +
616B LYS* 3.4 18.6 - - - -
618B ASN* 1.3 82.1 + - - +
620B ALA* 1.3 60.2 + - - +
625B VAL* 5.1 5.4 - - + -
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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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396B CYS* 5.2 4.3 - - - -
552B TYR* 3.5 32.5 - - + +
616B LYS 4.2 11.4 - - - +
617B PHE* 2.7 11.9 + - - +
619B VAL* 1.3 79.6 - - + +
621B MET* 1.3 76.5 - - + +
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Residues in contact with MET 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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552B TYR* 3.8 11.3 - - - +
617B PHE* 3.3 50.7 - - + +
618B ASN* 3.4 14.8 - - - +
620B ALA* 1.3 114.2 - - + +
622B GLY* 1.3 58.9 + - - +
623B ILE* 4.2 14.8 - - + -
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Residues in contact with GLY 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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552B TYR* 3.9 19.2 + - - -
555B HIS* 3.9 9.1 - - - +
556B CYS* 4.4 7.0 - - - -
559B ARG* 3.4 34.3 + - - +
618B ASN 2.9 2.8 + - - -
620B ALA 3.9 0.4 - - - -
621B MET* 1.3 78.6 - - - +
623B ILE* 1.3 66.2 + - - +
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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