Contacts of the helix formed by residues 617 - 632 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A LEU* 4.5 17.9 - - + -
576A LEU* 4.3 10.8 - - + -
615A PHE* 3.4 18.1 - - + +
616A ILE* 1.3 84.3 - - + -
618A PRO* 1.3 73.2 - - + +
619A LEU 3.2 2.0 - - - +
620A LEU* 3.0 27.1 + - + +
621A ALA 3.0 10.2 + - - -
646A GLN* 3.8 13.5 - - - +
761A VAL* 4.5 10.3 - - + -
765A VAL* 3.7 27.1 - - + -
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Residues in contact with PRO 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A TYR* 3.5 9.2 - - + +
566A THR* 5.9 1.1 - - + -
602A ASP* 4.5 4.7 - - - +
615A PHE* 4.5 2.9 - - + -
616A ILE 3.2 7.1 - - - +
617A PRO* 1.3 82.4 - - + +
619A LEU* 1.3 57.8 + - - +
621A ALA* 3.7 7.1 - - + +
622A VAL* 2.9 32.1 + - - +
642A VAL* 3.7 23.6 - - + +
644A THR* 3.3 28.0 - - + +
646A GLN* 3.4 39.0 - - + +
656A LEU* 3.9 3.8 - - + +
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Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LEU* 4.4 9.4 - - + -
492A TYR* 3.9 32.8 - - + +
495A PHE* 3.6 36.8 - - + -
617A PRO* 3.2 1.6 - - + +
618A PRO* 1.3 81.7 - - - +
620A LEU* 1.3 61.6 + - - +
622A VAL* 4.1 1.1 - - + -
623A GLY 3.1 17.5 + - - -
655A CYS* 3.7 35.4 - - + +
656A LEU* 3.6 16.0 - - + +
659A TYR* 4.0 20.2 - - + -
746A PHE* 3.5 13.6 - - + -
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Residues in contact with LEU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LEU* 3.7 13.7 - - + +
576A LEU* 3.9 24.9 - - + -
580A LEU* 3.5 37.2 - - + -
616A ILE* 4.1 2.0 - - + -
617A PRO* 3.0 13.5 + - + +
619A LEU* 1.3 78.3 - - - +
621A ALA* 1.3 64.1 + - - +
624A ALA* 3.0 28.0 + - + +
741A LEU* 3.7 24.7 - - + -
744A TYR* 5.1 3.1 - - + -
745A ALA* 3.7 20.6 - - + +
746A PHE* 4.1 8.1 - - + -
758A ILE* 5.4 1.6 - - + -
761A VAL* 4.1 13.5 - - + -
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Residues in contact with ALA 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A THR* 3.8 26.2 - - + -
580A LEU* 4.6 0.7 - - - -
583A LEU* 3.8 13.9 - - + -
600A LEU* 4.4 6.1 - - + -
616A ILE* 3.8 15.4 - - + +
617A PRO 3.0 11.5 + - - +
618A PRO* 3.3 11.4 + - + +
620A LEU* 1.3 77.6 - - - +
622A VAL* 1.3 58.0 + - - +
624A ALA* 3.7 1.4 - - - +
625A VAL* 2.8 35.0 + - - +
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A LEU* 4.0 15.0 - - + +
618A PRO 2.9 21.1 + - - +
619A LEU* 3.6 15.5 - - + +
621A ALA* 1.3 73.1 - - - +
623A GLY* 1.3 61.3 + - - +
625A VAL* 3.3 0.3 + - - -
626A HIS* 2.8 36.4 + - - +
640A LEU* 3.9 17.1 - - + +
642A VAL* 5.2 6.7 - - + -
656A LEU* 3.9 24.7 - - + +
659A TYR 3.9 4.9 - - - +
660A GLY 3.9 5.8 - - - -
661A ALA* 3.6 33.2 - - + +
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Residues in contact with GLY 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A LEU 3.1 17.1 + - - -
620A LEU 4.1 0.4 - - - -
622A VAL* 1.3 76.4 - - - +
624A ALA* 1.3 56.4 + - - +
626A HIS* 3.6 0.3 - - - +
627A HIS* 2.9 31.2 + - - +
659A TYR* 3.7 17.5 - - - -
745A ALA* 3.1 28.4 - - - +
746A PHE* 4.6 0.4 - - - -
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Residues in contact with ALA 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580A LEU* 3.8 13.0 - - + -
583A LEU* 5.1 0.4 - - + -
584A VAL* 4.0 7.2 - - + -
620A LEU 3.0 18.2 + - - +
621A ALA 3.7 3.8 - - - +
623A GLY* 1.3 76.7 - - - +
625A VAL* 1.3 59.7 + - + +
628A HIS* 2.9 35.7 + - - +
744A TYR* 3.8 36.1 - - + -
745A ALA* 3.4 7.8 - - + +
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Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A LEU* 3.7 24.2 - - + -
584A VAL* 4.4 8.1 - - + -
587A ALA* 4.0 21.1 - - + -
598A LEU* 4.4 1.6 - - + -
600A LEU* 3.8 20.6 - - + -
621A ALA 2.8 25.5 + - - +
622A VAL 4.5 0.2 - - - +
624A ALA* 1.3 73.1 - - - +
626A HIS* 1.3 65.5 + - - +
628A HIS* 4.5 1.1 - - - +
629A LEU* 2.9 38.7 + - + +
640A LEU* 3.5 33.2 - - + -
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Residues in contact with HIS 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 5.1 4.8 + - + +
239A TRP* 4.0 23.6 - + - -
622A VAL 2.8 23.2 + - - +
623A GLY 3.6 2.0 - - - +
625A VAL* 1.3 76.0 - - - +
627A HIS* 1.3 87.0 + + - +
629A LEU* 3.7 2.8 - - - +
630A ILE* 3.1 46.8 + - + +
635A ARG* 2.9 34.3 + - - +
640A LEU* 3.9 8.9 - - + +
659A TYR 3.4 23.2 - - - +
660A GLY* 3.7 10.7 - - - -
728A GLY* 4.6 11.4 + - - -
730A GLN* 4.5 6.8 + - - -
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Residues in contact with HIS 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 4.2 15.0 - - - -
623A GLY* 2.9 16.4 + - - +
626A HIS* 1.3 90.5 - + - +
628A HIS* 1.3 57.8 + - - +
630A ILE* 3.2 14.9 + - + +
631A ARG* 2.9 49.6 + - - +
659A TYR* 5.3 0.7 - + - -
730A GLN* 2.8 32.3 + - - -
744A TYR 4.2 8.5 - - - +
745A ALA 3.3 28.9 - - - -
746A PHE 4.1 0.4 - - - -
747A ALA* 3.6 31.9 + - + +
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Residues in contact with HIS 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A VAL* 3.5 39.8 - - + +
588A ILE* 4.2 7.1 - - + +
624A ALA 2.9 29.5 + - - +
625A VAL* 4.4 1.3 - - - +
627A HIS* 1.3 74.8 - - + +
629A LEU* 1.3 61.6 + - + +
631A ARG* 3.4 22.1 + - - +
632A ALA* 2.9 29.4 + - - +
744A TYR* 3.4 58.2 + + - -
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Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A VAL 5.3 0.2 - - - +
587A ALA* 4.3 9.9 - - + -
588A ILE* 3.9 36.3 - - + +
591A VAL* 4.4 16.2 - - + -
598A LEU* 4.6 0.7 - - + -
625A VAL* 2.9 36.8 + - + +
626A HIS 3.7 4.3 - - - +
628A HIS* 1.3 74.7 - - + +
630A ILE* 1.3 62.0 + - - +
632A ALA* 3.3 3.6 + - - -
633A GLY 3.1 3.5 + - - -
634A LEU* 2.9 44.7 + - + +
635A ARG* 3.3 25.2 + - - +
638A ALA* 5.5 4.0 - - + -
640A LEU* 3.9 15.9 - - + -
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Residues in contact with ILE 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ASN* 4.8 20.9 - - + +
239A TRP* 6.1 0.9 - - + -
242A ALA* 5.3 11.8 - - + +
245A LYS* 4.7 6.8 + - - -
626A HIS* 3.1 52.6 + - + +
627A HIS* 3.2 24.4 + - + +
629A LEU* 1.3 73.6 - - - +
631A ARG* 1.3 70.4 + - + +
633A GLY* 3.0 15.0 + - - -
635A ARG* 3.7 22.7 - - + -
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Residues in contact with ARG 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LYS* 5.7 2.3 - - - -
627A HIS* 2.9 36.1 + - - +
628A HIS* 3.6 23.9 + - - +
630A ILE* 1.3 82.4 - - + +
632A ALA* 1.3 57.9 + - - +
633A GLY 3.3 1.1 + - - -
743A GLU* 2.7 49.2 + - - +
744A TYR* 4.2 3.2 + - - +
747A ALA* 3.8 16.8 - - - +
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Residues in contact with ALA 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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588A ILE* 4.1 20.6 - - + -
628A HIS 2.9 17.5 + - - +
629A LEU* 3.8 5.2 - - - +
630A ILE 3.2 0.4 - - - -
631A ARG* 1.3 75.6 - - - +
633A GLY* 1.3 61.6 + - - +
634A LEU* 3.2 29.0 + - + +
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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