Contacts of the helix formed by residues 615 - 625 (chain A) in PDB entry 3QFS
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 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566A TYR* 2.7 37.4 + - - +
593A GLN* 3.9 6.8 + - - -
595A ASN* 3.6 12.8 + - - +
611A LEU* 3.1 13.6 + - - +
612A LEU 3.0 8.3 + - - +
614A GLN* 1.3 83.6 - - - +
616A ARG* 1.3 65.0 + - - +
617A GLU* 3.1 4.0 + - - -
618A HIS* 3.3 9.2 + - + +
619A LEU* 3.1 22.4 + - + +
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Residues in contact with ARG 616 (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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612A LEU 3.1 5.2 + - - -
613A LYS* 2.7 61.8 + - - +
614A GLN* 3.4 6.5 + - - +
615A ASP* 1.3 76.7 - - - +
617A GLU* 1.3 74.3 + - + +
619A LEU* 4.6 0.7 - - - -
620A TRP* 3.0 26.3 + - - +
649A ILE* 3.8 25.7 - - + +
652A GLU* 2.6 48.0 + - - -
653A LEU* 3.9 16.1 - - + +
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Residues in contact with GLU 617 (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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614A GLN 6.1 0.7 - - - +
615A ASP 3.1 1.4 + - - -
616A ARG* 1.3 88.1 - - + +
618A HIS* 1.3 63.0 + - - +
620A TRP* 3.4 4.7 + - - +
621A LYS* 3.2 20.4 + - - +
653A LEU* 4.4 18.3 - - + +
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Residues in contact with HIS 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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562A GLU* 2.7 40.3 + - - -
564A LEU* 4.1 7.6 - - + -
593A GLN* 3.6 23.1 + - - -
615A ASP* 3.3 10.7 + - + +
617A GLU* 1.3 76.1 - - - +
619A LEU* 1.3 66.7 + - + +
621A LYS* 3.1 24.9 + - + +
622A LEU* 2.9 48.5 + - + +
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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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532A ILE* 3.8 25.4 - - + -
564A LEU* 4.1 13.7 - - + -
566A TYR* 3.5 30.3 - - + +
612A LEU* 3.3 50.9 - - + +
615A ASP* 3.1 12.6 + - + +
616A ARG* 4.0 3.8 - - - +
618A HIS* 1.3 77.1 - - + +
620A TRP* 1.3 57.8 + - - +
622A LEU* 3.2 5.5 + - + +
623A ILE* 2.8 42.0 + - + +
646A PHE* 4.6 4.3 - - + -
649A ILE* 4.2 11.7 - - + -
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Residues in contact with TRP 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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616A ARG 3.0 18.8 + - - +
617A GLU 3.6 4.5 - - - +
619A LEU* 1.3 76.2 - - - +
621A LYS* 1.3 62.0 + - - +
623A ILE* 3.2 8.4 + - + +
624A GLU* 2.8 68.6 + - + +
649A ILE* 4.4 6.0 - - + +
650A VAL* 3.5 45.5 - - + -
653A LEU* 3.4 42.7 + - + -
654A GLY* 3.6 22.7 - - - -
656A MET* 4.4 3.4 - - + -
664A TYR* 3.9 20.0 - + - -
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Residues in contact with LYS 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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617A GLU 3.2 10.9 + - - +
618A HIS* 3.1 28.8 + - + +
620A TRP* 1.3 84.6 - - - +
622A LEU* 1.3 58.4 + - + +
624A GLU* 3.4 4.9 + - - +
625A GLY* 3.0 24.9 + - - -
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Residues in contact with LEU 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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530A PRO* 4.0 25.2 - - + +
532A ILE* 4.1 13.9 - - + -
562A GLU* 3.8 24.5 - - + +
564A LEU* 3.8 32.8 - - + -
618A HIS* 2.9 37.9 + - + +
619A LEU* 3.6 9.0 - - + +
621A LYS* 1.3 79.6 - - + +
623A ILE* 1.3 59.9 + - - +
625A GLY* 3.1 9.3 + - - -
626A GLY 3.3 0.5 + - - -
627A ALA* 2.9 32.7 + - + +
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Residues in contact with ILE 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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532A ILE* 4.1 10.1 - - + -
619A LEU* 2.8 30.6 + - + +
620A TRP* 3.6 11.7 - - + +
622A LEU* 1.3 69.0 - - - +
624A GLU* 1.3 64.5 + - - +
626A GLY 2.9 1.7 + - - -
627A ALA* 4.3 3.1 - - + +
629A ILE* 3.7 29.8 - - + -
646A PHE* 4.1 18.8 - - + -
649A ILE* 5.2 3.1 - - + -
650A VAL* 4.8 13.0 - - + -
664A TYR* 3.6 31.2 + - + +
665A ILE* 5.6 0.2 - - + -
668A LEU* 4.2 9.0 - - + -
673A ARG* 2.6 38.8 + - - +
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Residues in contact with GLU 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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620A TRP* 2.8 63.2 + - + +
621A LYS* 3.8 5.8 - - - +
623A ILE* 1.3 74.0 - - - +
625A GLY* 1.3 57.4 + - - +
626A GLY* 3.3 3.8 + - - -
664A TYR* 2.7 30.7 + - - -
673A ARG* 5.5 0.9 + - - -
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Residues in contact with GLY 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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530A PRO* 5.0 8.0 - - - +
621A LYS 3.0 14.7 + - - -
622A LEU* 3.1 7.8 + - - -
623A ILE 3.0 1.0 - - - -
624A GLU* 1.3 77.7 - - - +
626A GLY* 1.3 57.4 + - - +
627A ALA 3.6 0.4 - - - -
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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