Contacts of the helix formed by residues 617 - 630 (chain A) in PDB entry 5HLB
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A ALA 3.9 7.6 - - - -
502A MET 3.5 25.7 + - - +
503A GLN 4.2 2.5 - - - -
504A ALA 3.4 17.0 - - - +
505A ARG* 3.7 25.8 - - + +
616A LEU* 1.3 74.2 - - - +
618A PRO* 1.4 74.4 - - - +
619A ILE* 3.5 7.6 - - - +
620A GLU* 3.0 39.3 + - - +
621A VAL* 3.2 11.5 + - - +
709A TRP* 4.6 0.4 - - - -
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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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473A ALA* 3.8 20.6 - - + +
475A VAL* 3.8 19.1 - - + -
500A ARG 3.2 26.9 - - - +
501A ALA* 3.4 7.2 - - - +
504A ALA* 3.7 7.0 - - + +
617A THR* 1.4 79.1 - - - +
619A ILE* 1.4 55.1 + - - +
621A VAL* 3.3 4.8 + - + +
622A ALA* 3.0 27.2 + - - +
709A TRP* 4.1 10.0 - - + -
720A ILE* 3.7 25.6 - - + +
722A TRP* 4.2 17.3 - - + -
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Residues in contact with ILE 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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417A LEU* 4.0 28.9 - - + -
475A VAL* 3.9 8.2 - - + +
484A VAL* 4.6 6.5 - - + -
487A MET* 3.6 28.7 - - + -
501A ALA 3.1 22.6 + - - +
502A MET* 3.9 18.4 - - + +
617A THR* 3.5 10.5 - - - +
618A PRO* 1.4 75.3 - - - +
620A GLU* 1.3 65.7 + - + +
622A ALA* 3.3 15.1 + - - +
623A GLN* 3.3 10.0 + - - +
637A LEU* 3.4 25.5 - - + +
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Residues in contact with GLU 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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505A ARG* 2.7 43.9 + - - -
597A GLY 6.0 0.9 - - - +
598A VAL* 4.2 7.3 - - - +
599A PRO* 3.5 33.7 - - + +
616A LEU* 3.4 16.4 - - + +
617A THR* 3.0 28.9 + - - +
619A ILE* 1.3 77.3 - - + +
621A VAL* 1.3 64.0 + - - +
623A GLN* 3.4 15.5 + - - +
624A ALA* 3.4 13.0 + - - +
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Residues in contact with VAL 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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508A ILE* 3.7 29.2 - - + -
511A LEU* 3.5 27.1 - - + -
616A LEU* 3.8 13.2 - - + -
617A THR 3.2 13.2 + - - +
618A PRO 3.4 7.9 - - - +
620A GLU* 1.3 76.8 - - - +
622A ALA* 1.4 60.5 + - - +
624A ALA* 3.3 5.3 + - - +
625A PHE* 3.1 39.8 + - + -
709A TRP* 4.0 13.2 - - + -
720A ILE* 3.7 15.7 - - + -
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Residues in contact with ALA 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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475A VAL* 3.8 25.1 - - + +
477A VAL* 4.0 14.1 - - + +
618A PRO 3.0 13.6 + - - +
619A ILE 3.3 11.2 + - - +
621A VAL* 1.4 75.5 - - - +
623A GLN* 1.3 55.4 + - - +
625A PHE 3.8 0.3 + - - -
626A GLN* 3.0 28.9 + - - +
637A LEU* 4.0 9.9 - - + -
718A VAL* 4.1 3.6 - - + +
720A ILE* 3.5 17.9 - - + +
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Residues in contact with GLN 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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596A LEU 3.6 10.5 - - - +
597A GLY* 3.9 19.7 - - - +
619A ILE 3.3 4.7 + - - +
620A GLU* 3.6 11.9 - - - +
621A VAL 3.3 0.4 - - - -
622A ALA* 1.3 76.1 - - - +
624A ALA* 1.4 58.2 + - - +
626A GLN* 3.2 17.0 + - - +
627A THR* 2.9 37.8 + - - -
634A ARG* 4.0 8.2 - - - +
635A ALA 2.9 26.7 + - - -
636A PRO* 3.3 8.3 - - - +
637A LEU* 3.0 41.1 + - + +
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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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593A TRP* 4.1 13.5 - - + -
596A LEU* 3.5 25.3 + - + +
598A VAL* 3.8 27.1 - - + +
620A GLU 3.4 3.4 + - - +
621A VAL* 3.3 11.8 + - - +
623A GLN* 1.4 80.2 - - - +
625A PHE* 1.3 64.1 + - + +
627A THR* 3.6 8.7 + - - -
628A ILE* 3.3 21.8 - - - +
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Residues in contact with PHE 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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508A ILE* 6.2 0.7 - - + -
511A LEU* 3.3 43.5 - - + -
514A PRO* 4.1 18.6 - - + -
593A TRP* 5.9 2.2 - + - -
621A VAL* 3.1 46.9 + - + +
624A ALA* 1.3 79.1 - - + +
626A GLN* 1.4 58.8 - - - +
628A ILE* 3.4 12.4 + - + +
629A ALA* 2.9 29.8 + - - +
674A MET* 4.0 26.9 - - + -
698A LYS* 4.5 3.1 - - + -
711A ALA* 3.9 18.8 - - + -
713A ILE* 4.5 5.8 - - + +
718A VAL* 3.8 22.4 - - + -
720A ILE* 3.9 6.5 - - + -
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Residues in contact with GLN 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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477A VAL* 4.2 9.2 - - + -
478A ASP 3.7 14.4 - - - +
479A ARG* 3.0 26.4 + - - +
480A PHE 3.6 5.5 + - - -
482A GLY* 4.1 8.5 - - - -
622A ALA 3.0 21.4 + - - +
623A GLN* 3.2 12.6 + - - +
625A PHE* 1.4 76.0 - - - +
627A THR* 1.4 67.0 + - - +
630A SER* 3.0 26.6 + - - -
633A ASN 3.5 13.1 + - - -
635A ALA* 2.9 47.6 + - - +
637A LEU* 4.4 1.8 - - + -
718A VAL* 3.9 10.7 - - - +
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Residues in contact with THR 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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595A LYS 3.7 6.7 - - - +
596A LEU* 2.7 38.3 + - + -
623A GLN 2.9 7.0 + - - -
624A ALA 3.6 7.0 - - - -
626A GLN* 1.4 76.4 + - - +
628A ILE* 1.4 55.9 + - - +
630A SER* 3.1 7.8 + - - -
632A GLY* 3.1 30.0 + - - +
633A ASN 3.3 9.8 + - - -
634A ARG* 3.5 33.1 - - + +
661A ALA* 3.7 21.8 - - + -
662A VAL* 5.1 1.3 - - + -
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Residues in contact with ILE 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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514A PRO* 6.0 5.4 - - + -
518A LEU* 4.2 14.6 - - + -
596A LEU* 3.7 22.2 - - + -
624A ALA 3.3 19.1 - - - +
625A PHE* 3.4 14.3 + - + +
626A GLN 3.2 0.4 - - - -
627A THR* 1.4 71.7 - - - +
629A ALA* 1.4 64.8 + - - +
630A SER 3.2 2.2 - - - -
631A GLY* 3.2 12.8 + - - -
632A GLY* 4.5 2.7 - - - +
662A VAL* 5.4 0.7 - - - -
667A ALA* 3.5 33.8 - - + +
670A THR* 3.7 27.1 - - + -
671A LEU* 3.3 32.3 - - + +
674A MET* 4.4 9.9 - - - -
713A ILE* 5.2 2.0 - - + -
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Residues in contact with ALA 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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479A ARG* 2.7 45.0 + - + -
625A PHE 2.9 22.3 + - - +
626A GLN 3.8 2.0 - - - +
628A ILE* 1.4 72.2 - - - +
630A SER* 1.4 54.1 + - - +
631A GLY 3.2 2.6 + - - -
671A LEU* 4.0 14.9 - - - +
713A ILE* 3.8 18.4 - - + -
718A VAL* 3.6 24.5 - - + -
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Residues in contact with SER 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ARG* 3.4 20.8 + - - -
480A PHE* 4.1 32.2 - - - -
626A GLN* 3.0 15.3 + - - -
627A THR 3.1 4.3 + - - -
628A ILE 3.2 0.2 - - - -
629A ALA* 1.4 74.5 - - - +
631A GLY* 1.3 57.4 + - - +
633A ASN* 2.5 48.9 + - - -
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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