Contacts of the helix formed by residues 617 - 632 (chain B) in PDB entry 1OFD
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 PRO 617 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B LEU* 4.3 23.3 - - + +
576B LEU* 4.4 8.1 - - + -
615B PHE* 3.4 18.8 - - + +
616B ILE* 1.3 86.1 - - + +
618B PRO* 1.3 68.5 - - + +
619B LEU* 3.2 2.0 - - + +
620B LEU* 3.1 12.1 + - + +
621B ALA 2.9 23.2 + - - -
646B GLN* 3.8 14.1 - - - +
761B VAL* 4.3 12.6 - - + -
765B VAL* 3.7 26.5 - - + -
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Residues in contact with PRO 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B TYR* 3.5 7.9 - - + +
566B THR* 6.1 0.9 - - + -
602B ASP* 4.7 1.6 - - - +
615B PHE* 4.5 3.8 - - + -
616B ILE 3.3 6.0 - - - +
617B PRO* 1.3 83.3 - - + +
619B LEU* 1.3 57.3 + - - +
621B ALA* 3.8 7.1 - - + +
622B VAL* 2.9 33.6 + - - +
642B VAL* 3.7 24.4 - - + +
644B THR* 3.4 21.3 - - + +
646B GLN* 3.4 46.2 - - + +
656B LEU* 3.8 5.2 - - + -
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Residues in contact with LEU 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 4.5 10.8 - - + -
492B TYR* 4.0 32.8 - - + +
495B PHE* 3.4 37.7 - - + -
617B PRO* 3.2 1.3 - - + -
618B PRO* 1.3 80.7 - - - +
620B LEU* 1.3 58.4 + - - +
622B VAL* 3.5 0.8 - - + +
623B GLY 3.1 22.9 + - - -
655B CYS* 3.8 33.9 - - + +
656B LEU* 3.5 15.0 - - + +
659B TYR* 4.0 13.7 - - + -
746B PHE* 3.6 20.6 - - + -
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Residues in contact with LEU 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 3.7 14.6 - - + +
576B LEU* 4.0 20.9 - - + -
580B LEU* 3.6 33.9 - - + -
616B ILE* 4.1 7.9 - - + -
617B PRO* 3.1 11.9 + - + +
619B LEU* 1.3 77.9 - - - +
621B ALA* 1.3 59.4 - - - +
624B ALA* 2.9 34.2 + - + +
741B LEU* 3.6 26.2 - - + -
744B TYR* 5.2 2.0 - - + -
745B ALA* 3.5 25.7 - - + +
746B PHE* 3.9 9.2 - - + -
758B ILE* 5.2 0.9 - - + -
761B VAL* 4.1 14.8 - - + -
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Residues in contact with ALA 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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566B THR* 3.9 20.9 - - + -
583B LEU* 3.8 24.0 - - + -
600B LEU* 4.3 6.3 - - + -
616B ILE* 3.7 12.7 - - + +
617B PRO 2.9 15.0 + - - +
618B PRO* 3.8 8.3 - - + +
620B LEU* 1.3 75.7 - - - +
622B VAL* 1.3 60.1 + - - +
624B ALA* 3.9 1.3 - - - +
625B VAL* 3.0 32.8 + - - +
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Residues in contact with VAL 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LEU* 3.9 15.4 - - + +
618B PRO 2.9 24.2 + - - +
619B LEU* 3.5 14.6 - - + +
621B ALA* 1.3 70.8 - - - +
623B GLY* 1.3 62.6 + - - +
625B VAL 3.4 1.0 + - - -
626B HIS* 2.8 32.1 + - - +
640B LEU* 3.9 17.0 - - + +
642B VAL* 5.2 7.2 - - + -
656B LEU* 4.0 25.8 - - + +
659B TYR 3.9 4.3 - - - +
660B GLY 3.9 4.7 - - - -
661B ALA* 3.6 36.6 - - + +
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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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619B LEU 3.1 17.2 + - - -
620B LEU 4.0 0.2 - - - -
622B VAL* 1.3 77.6 - - - +
624B ALA* 1.3 62.5 + - - +
626B HIS* 3.6 0.2 - - - +
627B HIS* 3.0 26.0 + - - +
659B TYR* 3.7 19.3 - - - -
745B ALA* 3.1 27.4 - - - +
746B PHE* 4.6 0.4 - - - -
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Residues in contact with ALA 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B LEU* 3.9 14.4 - - + -
584B VAL* 4.0 5.8 - - + -
620B LEU 2.9 19.1 + - - +
621B ALA 3.9 2.5 - - - +
623B GLY* 1.3 77.3 - - - +
625B VAL* 1.3 57.7 + - + +
628B HIS* 2.8 35.3 + - - -
744B TYR* 3.7 32.5 - - + -
745B ALA* 3.5 12.3 - - + +
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Residues in contact with VAL 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B LEU* 3.8 32.5 - - + -
584B VAL* 4.3 11.0 - - + -
587B ALA* 4.1 20.4 - - + -
600B LEU* 4.0 14.8 - - + -
621B ALA 3.0 18.2 + - - +
622B VAL 4.1 0.7 - - - +
624B ALA* 1.3 74.7 - - - +
626B HIS* 1.3 58.7 + - - +
628B HIS* 4.5 0.9 - - - +
629B LEU* 2.8 42.2 + - + +
640B LEU* 3.5 35.4 - - + -
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Residues in contact with HIS 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 5.0 5.0 + - + +
239B TRP* 4.0 22.7 - + - -
622B VAL 2.8 22.4 + - - +
623B GLY 3.6 1.6 - - - +
625B VAL* 1.3 71.0 - - - +
627B HIS* 1.3 82.9 + + - +
629B LEU* 3.5 2.8 + - - +
630B ILE* 3.1 48.9 + - + +
635B ARG* 2.9 39.4 + - - +
640B LEU* 4.0 9.4 - - + -
659B TYR 3.4 23.2 - - - +
660B GLY* 3.7 8.5 - - - -
728B GLY* 4.6 12.1 + - - -
730B GLN* 4.5 7.0 + - - -
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Residues in contact with HIS 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ASN* 4.3 13.9 - - - -
623B GLY* 3.0 17.3 + - - +
626B HIS* 1.3 89.2 - + - +
628B HIS* 1.3 60.3 + - - +
630B ILE* 3.3 14.7 + - + +
631B ARG* 3.0 44.8 + - - +
659B TYR* 5.2 0.7 - + - -
730B GLN* 2.8 33.6 + - - -
744B TYR 4.1 13.7 - - - +
745B ALA 3.3 29.1 + - - -
746B PHE 4.0 0.6 - - - -
747B ALA* 3.5 33.6 + - + +
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Residues in contact with HIS 628 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B VAL* 3.6 37.4 - - + +
588B ILE* 4.0 10.8 - - + +
624B ALA* 2.8 32.6 + - - +
625B VAL* 4.2 1.6 - - - +
627B HIS* 1.3 73.5 - - + +
629B LEU* 1.3 60.3 + - - +
631B ARG* 3.4 21.8 + - - +
632B ALA* 3.0 29.3 + - - +
744B TYR* 3.3 57.0 + + - -
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Residues in contact with LEU 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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587B ALA* 4.5 2.5 - - + +
588B ILE* 3.9 27.6 - - + +
591B VAL* 4.0 27.4 - - + -
598B LEU* 4.6 2.5 - - + -
625B VAL* 2.8 27.3 + - + +
626B HIS 3.7 4.5 - - - +
628B HIS* 1.3 74.0 - - - +
630B ILE* 1.3 63.2 + - - +
632B ALA* 3.4 2.7 + - - -
633B GLY 3.0 3.5 + - - -
634B LEU* 2.8 50.8 + - + +
635B ARG* 3.3 21.7 + - - +
638B ALA* 5.8 2.9 - - + +
640B LEU* 3.9 28.3 - - + -
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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
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238B ASN* 4.8 22.7 - - + +
239B TRP* 6.3 0.7 - - + -
242B ALA* 5.2 13.7 - - + -
245B LYS* 4.7 4.7 + - - -
626B HIS* 3.1 51.7 + - + +
627B HIS* 3.3 20.4 + - + +
629B LEU* 1.3 74.3 - - - +
631B ARG* 1.3 60.7 + - + +
633B GLY* 2.7 25.9 + - - -
635B ARG* 3.7 21.5 - - + +
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Residues in contact with ARG 631 (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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245B LYS* 5.7 2.9 - - - -
627B HIS* 3.0 37.7 + - - +
628B HIS* 3.7 24.7 - - + +
629B LEU 3.4 0.2 - - - -
630B ILE* 1.3 80.0 - - + +
632B ALA* 1.3 58.3 + - - +
633B GLY 3.5 0.2 + - - -
743B GLU* 2.6 50.9 + - - -
744B TYR* 4.3 1.2 + - - +
747B ALA* 3.6 18.0 - - - +
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Residues in contact with ALA 632 (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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245B LYS* 5.7 0.9 - - - -
588B ILE* 4.2 20.9 - - + -
628B HIS 3.0 16.6 + - - +
629B LEU 4.0 4.0 - - - +
630B ILE 3.2 0.2 - - - -
631B ARG* 1.3 75.2 - - - +
633B GLY* 1.3 61.6 + - - +
634B LEU* 3.4 22.5 + - + +
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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