Contacts of the helix formed by residues 617 - 626 (chain B) in PDB entry 3FA2
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 THR 617 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B PO4 3.2 25.8 - - - +
575B SER* 2.9 19.5 + - - +
576B GLY* 6.0 0.9 - - - -
615B GLN* 2.9 19.8 + - + -
616B SER* 1.3 78.5 - - - +
618B LEU* 1.3 64.8 + - - +
619B LYS 4.1 2.5 - - - -
620B CYS* 3.1 17.7 + - - +
621B MET* 2.9 27.6 + - - +
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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 SER 4.2 0.4 + - - -
617B THR* 1.3 73.4 - - - +
619B LYS* 1.3 58.8 + - + +
621B MET* 4.3 6.8 - - + +
622B LEU* 2.8 59.0 + - + +
686B HIS* 5.6 1.6 - - - -
690B ASN* 3.3 56.3 - - + +
693B LYS* 4.5 20.4 - - + +
694B LEU* 4.5 12.6 - - + -
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Residues in contact with LYS 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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1B PO4 2.6 41.4 + - - +
573B ILE* 3.6 24.0 - - + -
574B GLY 3.8 11.4 - - - +
575B SER* 4.2 13.2 - - - +
598B THR 3.1 27.4 - - - -
599B GLU* 4.6 6.9 + - - +
600B PHE* 4.0 24.3 - - + +
607B VAL* 4.4 8.6 - - + +
617B THR* 3.2 2.1 + - - +
618B LEU* 1.3 79.4 - - + +
620B CYS* 1.3 57.1 + - - +
622B LEU* 4.6 3.1 - - - -
623B GLY* 2.9 24.8 + - - -
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Residues in contact with CYS 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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575B SER* 3.4 14.8 - - - -
607B VAL* 4.3 9.6 - - - -
609B VAL* 3.4 33.2 - - - -
614B VAL* 3.8 13.7 - - + -
615B GLN* 3.2 26.9 - - - +
617B THR* 3.1 23.5 + - - +
619B LYS* 1.3 74.2 - - - +
621B MET* 1.3 58.7 + - - +
623B GLY* 3.2 1.2 + - - -
624B ILE* 2.8 33.6 + - - +
630B ILE* 4.1 4.3 - - + +
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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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616B SER* 4.1 11.2 - - - +
617B THR 2.9 24.6 + - - +
618B LEU* 4.0 7.4 - - + +
620B CYS* 1.3 71.6 - - - +
622B LEU* 1.3 62.0 + - - +
624B ILE* 3.2 5.3 + - - +
625B LEU* 2.8 35.9 + - - +
686B HIS* 3.9 17.9 - - + -
690B ASN* 5.8 0.4 - - - +
694B LEU* 3.4 37.5 - - + -
764B ILE* 3.6 27.6 - - + -
767B VAL* 3.7 17.0 - - + +
768B MET* 3.5 31.0 - - - +
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Residues in contact with LEU 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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600B PHE* 3.4 37.2 - - + +
618B LEU* 2.8 46.3 + - + +
619B LYS 4.1 1.3 - - - +
621B MET* 1.3 73.5 - - - +
623B GLY* 1.3 56.8 + - - +
625B LEU* 3.5 4.3 + - + +
626B ASN* 3.0 29.5 + - - +
693B LYS* 4.0 23.6 - - + +
694B LEU* 4.0 15.0 - - + -
697B ALA* 3.5 30.5 - - + +
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Residues in contact with GLY 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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600B PHE* 3.7 16.3 - - - -
607B VAL* 4.2 1.3 - - - -
619B LYS 2.9 20.1 + - - -
620B CYS 3.5 2.2 - - - -
621B MET 3.1 0.6 - - - -
622B LEU* 1.3 72.9 - - - +
624B ILE* 1.3 64.5 + - - +
626B ASN 3.1 9.4 + - - -
628B CYS* 3.1 27.3 + - - +
630B ILE* 3.8 14.4 - - - -
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Residues in contact with ILE 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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614B VAL* 4.2 11.7 - - + -
620B CYS 2.8 21.7 + - - +
621B MET* 3.5 7.6 - - - +
623B GLY* 1.3 72.7 - - - +
625B LEU* 1.3 58.2 + - - +
627B GLY 2.8 10.2 + - - -
628B CYS 5.0 1.6 - - - +
630B ILE* 3.9 17.6 - - + +
656B GLY 4.6 4.0 - - - +
657B PRO* 4.1 14.4 - - + -
660B SER* 2.4 45.6 + - - -
767B VAL* 3.4 29.6 - - + +
768B MET* 4.0 36.3 - - + +
770B PHE* 4.1 10.5 - - + -
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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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621B MET 2.8 20.1 + - - +
622B LEU* 3.9 4.9 - - + +
624B ILE* 1.3 76.1 - - + +
626B ASN* 1.3 56.4 + - - +
627B GLY 3.4 0.2 - - - -
660B SER* 4.5 0.9 - - - -
670B LYS* 5.0 1.9 + - - +
671B LEU* 4.5 19.3 - - + -
672B PHE* 5.1 1.6 - - + -
694B LEU* 3.3 52.5 - - + +
697B ALA* 3.8 27.6 - - + +
698B GLY* 3.7 16.7 - - - +
767B VAL* 3.9 25.8 - - + -
770B PHE* 4.5 8.5 - - + -
778B GOL 3.4 25.1 - - - -
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Residues in contact with ASN 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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600B PHE* 3.8 13.1 - - + -
602B SER* 3.0 40.4 + - - +
604B VAL 3.5 17.2 + - - -
622B LEU 3.0 17.4 + - - +
623B GLY 3.6 4.7 - - - +
624B ILE 3.0 0.6 - - - -
625B LEU* 1.3 78.7 - - - +
627B GLY* 1.3 59.9 + - - +
628B CYS* 3.7 5.5 - - - -
664B ARG* 3.0 38.2 + - - +
670B LYS* 5.5 5.0 + - - +
778B GOL 4.1 4.1 - - - -
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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