Contacts of the helix formed by residues 609 - 617 (chain B) in PDB entry 4F1P
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 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576B PHE* 3.6 4.8 - - - -
598B VAL 5.3 0.2 - - - -
599B ASN* 4.3 8.3 - - - +
600B TRP 3.4 8.7 - - - +
601B VAL* 4.7 0.4 - - + -
607B ASN 4.3 7.4 - - - +
608B ALA* 1.3 78.9 - - - +
610B PRO* 1.3 69.6 - - - +
611B LEU* 3.5 9.0 + - - +
612B ILE* 3.1 32.5 + - + +
613B GLN* 2.9 28.9 + - - +
635B GLN* 3.6 41.7 + - + +
636B ALA 5.5 0.7 - - - +
643B PRO* 5.3 0.5 - - - +
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Residues in contact with PRO 610 (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 LEU* 3.8 21.8 - - + +
576B PHE* 3.9 16.4 - - + +
579B SER* 3.5 26.0 - - - +
598B VAL 3.6 20.2 - - - +
600B TRP* 3.3 23.1 - - + +
609B THR* 1.3 86.4 - - - +
611B LEU* 1.3 51.5 + - - +
613B GLN* 3.2 8.5 + - + +
614B ALA* 2.8 31.7 + - - +
626B LEU* 3.6 17.9 - - + -
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Residues in contact with LEU 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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598B VAL 5.2 1.2 + - - +
599B ASN* 6.0 1.1 - - - +
609B THR* 3.2 8.2 + - - +
610B PRO* 1.3 76.6 - - - +
612B ILE* 1.3 60.3 + - - +
614B ALA* 3.2 2.9 + - - +
615B THR* 2.8 32.0 + - - -
623B CYS* 3.9 29.4 - - + +
626B LEU* 3.6 12.5 - - + +
627B LEU* 4.2 9.4 - - + -
631B ALA* 4.1 18.8 - - + -
632B ASN 3.7 19.5 - - - +
633B VAL* 3.9 11.7 - - + -
643B PRO* 3.6 29.4 - - + -
659B PHE* 3.9 20.9 - - + -
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Residues in contact with ILE 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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608B ALA* 3.9 16.6 - - + -
609B THR* 3.1 30.7 + - + +
611B LEU* 1.3 74.4 - - - +
613B GLN* 1.3 58.9 + - - +
615B THR* 3.3 8.1 + - - -
616B ALA* 3.0 28.1 + - + +
635B GLN 3.7 14.8 - - - +
636B ALA 4.3 0.7 - - - -
637B ASP* 3.8 14.6 - - + +
641B ARG 3.6 23.3 - - - +
643B PRO* 4.1 15.7 - - + -
646B HIS* 3.6 39.0 - - + +
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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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576B PHE* 3.2 58.1 + - + +
577B ARG* 4.7 4.4 + - - +
579B SER 3.9 0.2 - - - -
580B GLY* 3.4 23.5 - - - +
608B ALA* 5.5 2.1 - - - +
609B THR 2.9 13.9 + - - +
610B PRO* 3.2 14.8 - - + +
612B ILE* 1.3 77.8 - - - +
614B ALA* 1.3 56.2 + - - +
616B ALA* 3.3 10.8 + - - +
617B ALA* 3.0 26.3 + - - +
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Residues in contact with ALA 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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579B SER* 3.4 12.7 + - - +
610B PRO 2.8 18.4 + - - +
611B LEU 3.2 3.1 + - - +
613B GLN* 1.3 73.6 - - - +
615B THR* 1.3 57.0 + - - +
617B ALA* 3.3 3.4 + - - +
618B ASN 3.1 19.2 + - - -
619B SER 3.1 14.6 + - - +
622B ALA* 3.6 27.4 - - + -
623B CYS* 3.5 23.2 - - - +
626B LEU* 4.2 6.1 - - + -
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Residues in contact with THR 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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611B LEU 2.8 18.2 + - - -
612B ILE* 3.5 11.3 - - - -
613B GLN 3.2 0.2 - - - -
614B ALA* 1.3 72.7 - - - +
616B ALA* 1.3 60.4 + - - +
617B ALA 3.0 1.1 - - - -
618B ASN* 2.8 15.9 + - - -
623B CYS* 3.8 0.4 - - - -
643B PRO* 3.9 9.1 - - - +
646B HIS* 3.9 11.0 - - + +
647B ALA* 3.6 39.0 - - + +
650B LEU* 4.3 0.4 - - + -
652B HIS* 3.3 20.8 + - - +
655B LEU* 3.8 14.4 - - + -
659B PHE* 3.2 22.7 - - + -
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Residues in contact with ALA 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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581B HIS* 5.5 0.4 - - - +
612B ILE* 3.0 15.0 + - + +
613B GLN* 3.5 15.7 - - - +
615B THR* 1.3 75.8 - - - +
617B ALA* 1.3 58.9 + - - +
618B ASN* 3.2 1.4 + - - +
646B HIS* 5.7 2.4 + - - +
650B LEU* 3.8 18.9 - - + +
652B HIS* 4.4 6.4 - - - -
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Residues in contact with ALA 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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579B SER 3.9 6.1 - - - +
580B GLY 3.9 4.7 - - - -
581B HIS* 3.6 47.8 + - + +
583B PRO* 4.2 10.9 - - + +
613B GLN 3.0 13.6 + - - +
614B ALA* 3.4 10.3 - - - +
615B THR 3.0 0.2 - - - -
616B ALA* 1.3 74.7 - - - +
618B ASN* 1.3 70.9 + - - +
619B SER* 3.3 2.4 + - - -
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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