Contacts of the helix formed by residues 620 - 634 (chain A) in PDB entry 1QF6
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 ASP 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605A LYS* 3.4 34.6 + - - +
619A MET* 1.3 74.2 - - - +
621A VAL* 1.3 68.7 + - - +
622A ASN* 3.1 24.3 + - - +
623A GLU* 2.8 34.7 + - + +
624A VAL* 3.1 11.3 + - - +
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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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554A TYR* 4.5 0.2 - - - +
558A LEU* 3.5 29.2 - - + -
561A LYS* 3.5 35.2 - - + -
562A LEU* 5.3 2.7 - - + -
604A GLY 4.0 14.0 + - - +
605A LYS* 4.9 2.4 - - - +
606A VAL* 3.6 18.6 - - + -
619A MET 3.6 3.4 + - - -
620A ASP* 1.3 71.0 + - - +
622A ASN* 1.3 60.6 + - - +
623A GLU 2.7 11.4 + - - -
624A VAL* 2.8 31.6 + - + +
625A ILE* 3.2 12.4 + - + +
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Residues in contact with ASN 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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561A LYS* 3.3 30.5 + - - +
620A ASP* 3.1 11.4 + - - +
621A VAL* 1.3 81.2 - - - +
623A GLU* 1.3 59.2 + - - +
625A ILE* 3.9 11.3 - - - +
626A GLU* 3.3 28.6 + - - +
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Residues in contact with GLU 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 MET* 3.3 30.5 - - - +
620A ASP* 2.8 25.7 + - + +
621A VAL 2.7 6.1 + - - -
622A ASN* 1.3 72.9 - - - +
624A VAL* 1.3 59.0 + - - +
625A ILE 3.0 1.6 - - - -
626A GLU* 3.3 9.3 + - - +
627A LYS* 2.9 73.5 + - + +
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Residues in contact with VAL 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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562A LEU* 5.2 5.8 - - + -
594A LEU* 4.8 16.4 - - + -
606A VAL* 5.9 2.7 - - + -
608A VAL* 3.7 15.7 - - + -
619A MET* 3.3 41.1 - - + +
620A ASP 3.1 6.3 + - - +
621A VAL* 2.8 31.8 + - + +
623A GLU* 1.3 76.4 - - - +
625A ILE* 1.3 63.5 + - + +
627A LYS* 3.7 8.1 - - - +
628A LEU* 2.9 43.4 + - + +
640A LEU* 5.3 3.8 - - + -
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Residues in contact with ILE 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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561A LYS* 4.2 17.7 - - + +
562A LEU* 4.2 29.6 - - + -
565A ALA* 4.0 23.6 - - + -
567A ILE* 4.8 3.1 - - + -
621A VAL* 3.2 22.4 + - + +
622A ASN* 3.9 11.2 - - - +
623A GLU 3.0 1.0 - - - -
624A VAL* 1.3 76.6 - - + +
626A GLU* 1.3 69.5 + - + +
628A LEU* 3.1 6.3 + - - +
629A GLN* 3.0 53.9 + - + +
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Residues in contact with GLU 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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622A ASN* 3.3 16.4 + - - +
623A GLU* 3.3 11.2 + - + +
625A ILE* 1.3 79.9 - - + +
627A LYS* 1.3 65.7 + - + +
629A GLN* 3.5 13.9 + - - +
630A GLN* 3.1 23.1 + - - +
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Residues in contact with LYS 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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619A MET* 4.2 10.3 - - - +
623A GLU* 2.9 60.0 + - + +
624A VAL* 3.7 4.9 - - - +
625A ILE 3.1 0.2 - - - -
626A GLU* 1.3 79.7 - - + +
628A LEU* 1.3 60.9 + - - +
630A GLN* 3.5 7.8 - - - +
631A GLU* 3.2 19.8 + - - +
640A LEU* 3.8 42.5 - - + +
641A GLU* 3.0 23.7 + - - -
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Residues in contact with LEU 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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535A THR* 5.1 3.1 - - + -
541A GLN* 5.9 0.7 - - + -
542A VAL* 3.6 31.2 - - + -
562A LEU* 4.8 7.9 - - + -
567A ILE* 4.6 16.6 - - + -
592A TYR* 3.1 42.4 - - + -
594A LEU* 6.5 0.2 - - + -
624A VAL* 2.9 32.9 + - + +
625A ILE* 3.8 4.0 - - - +
627A LYS* 1.3 73.0 - - - +
629A GLN* 1.3 55.9 + - - +
630A GLN 2.6 16.2 + - - -
631A GLU* 2.7 20.5 + - - +
632A ILE* 2.8 26.9 + - + +
640A LEU* 4.6 8.5 - - + -
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Residues in contact with GLN 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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565A ALA* 2.9 33.7 + - - +
567A ILE* 4.1 7.6 - - + -
625A ILE* 3.0 41.5 + - + +
626A GLU* 3.9 11.6 - - - +
628A LEU* 1.3 75.0 - - - +
630A GLN* 1.3 56.6 + - - +
632A ILE* 4.0 11.3 - - - +
633A ARG* 3.0 30.2 + - - +
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Residues in contact with GLN 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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626A GLU 3.1 16.5 + - - +
627A LYS* 3.5 8.3 - - - +
628A LEU 2.6 5.1 + - - -
629A GLN* 1.3 72.9 - - - +
631A GLU* 1.3 66.4 + - - +
632A ILE 3.1 1.1 - - - -
633A ARG* 3.4 13.7 + - - +
634A SER* 3.0 40.5 + - - -
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Residues in contact with GLU 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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535A THR* 2.7 29.8 + - - +
536A TRP* 5.2 0.5 - - - +
592A TYR* 2.6 36.1 + - - -
627A LYS 3.2 10.2 + - - +
628A LEU* 2.7 16.0 + - - +
630A GLN* 1.3 76.4 - - - +
632A ILE* 1.3 64.3 + - + +
634A SER* 3.2 3.8 + - - -
635A ARG* 3.2 0.5 + - - -
636A SER* 3.0 49.8 + - - +
638A LYS 3.0 21.4 - - - +
639A GLN* 3.0 14.3 - - - +
640A LEU* 4.3 4.9 - - + +
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Residues in contact with ILE 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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535A THR* 4.2 16.4 - - + -
536A TRP* 4.1 18.1 - - + +
541A GLN* 3.2 37.7 - - - +
566A GLY 5.0 5.2 - - - +
567A ILE* 4.4 16.6 - - + -
628A LEU* 2.8 25.4 + - + +
629A GLN* 4.0 7.9 - - - +
631A GLU* 1.3 74.0 - - - +
633A ARG* 1.3 58.1 + - - +
634A SER 2.7 4.7 + - - -
635A ARG* 2.5 36.0 + - - +
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Residues in contact with ARG 633 (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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629A GLN 3.0 18.7 + - - +
630A GLN* 3.8 15.5 - - - +
632A ILE* 1.3 82.6 - - + +
634A SER* 1.3 72.5 + - - +
635A ARG* 3.4 10.0 + - - +
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Residues in contact with SER 634 (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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410A THR* 5.7 0.2 - - - +
630A GLN* 3.0 31.9 + - - -
631A GLU* 3.2 7.3 + - - -
632A ILE 2.7 2.8 + - - -
633A ARG* 1.3 90.5 - - - +
635A ARG* 1.3 69.2 + - - +
636A SER* 3.1 15.9 + - - -
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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