Contacts of the helix formed by residues 613 - 627 (chain A) in PDB entry 1Q99
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 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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614A LYS* 1.3 59.0 + - - +
615A ASP* 4.7 1.8 - - - -
616A ASP* 3.1 29.4 + - - +
617A ASP* 2.6 35.0 + - - +
652A ASN* 5.6 5.3 - - - +
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Residues in contact with LYS 614 (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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568A ARG* 4.2 21.9 + - - +
613A THR* 1.3 70.2 - - - +
615A ASP* 1.3 71.9 + - - +
616A ASP 3.0 1.6 - - - -
617A ASP* 2.8 21.5 + - - +
618A HIS* 3.0 9.9 + - - +
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Residues in contact with ASP 615 (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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568A ARG* 2.7 37.9 + - - +
571A ARG* 4.4 7.6 + - - -
576A LEU* 3.5 20.7 - - + +
613A THR* 4.7 1.1 - - - -
614A LYS* 1.3 78.8 - - - +
616A ASP* 1.3 64.5 + - - +
618A HIS* 3.2 2.9 + - - +
619A ILE* 3.0 28.1 + - - +
643A PHE* 3.4 27.1 - - + -
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Residues in contact with ASP 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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613A THR* 3.1 32.6 - - - +
614A LYS 2.9 0.6 + - - -
615A ASP* 1.3 78.1 - - - +
617A ASP* 1.3 62.7 + - - +
619A ILE* 3.3 4.2 + - - +
620A ALA* 3.2 16.3 + - - +
642A THR* 4.4 7.2 - - - +
643A PHE* 3.6 35.0 - - - +
650A LEU* 4.0 4.5 - - + +
651A ARG* 5.9 0.2 - - - +
652A ASN* 3.5 20.8 + - + +
653A ILE* 3.5 25.6 - - + +
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Residues in contact with ASP 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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613A THR 2.6 22.6 + - - +
614A LYS* 2.8 11.4 + - - +
616A ASP* 1.3 72.1 - - - +
618A HIS* 1.3 62.5 + - - +
620A ALA* 3.2 7.0 + - - +
621A GLN* 3.1 32.0 + - + +
653A ILE* 3.7 21.3 - - - +
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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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568A ARG* 3.4 57.3 + - - +
569A GLU* 4.4 6.9 + - - -
571A ARG 3.7 14.3 + - - -
576A LEU* 3.3 23.7 - - + +
604A PHE* 3.3 46.0 + + + +
614A LYS 3.0 5.5 + - - +
615A ASP 3.4 9.0 - - - +
617A ASP* 1.3 78.3 - - - +
619A ILE* 1.3 62.4 + - - +
621A GLN* 3.2 12.9 + - - +
622A ILE* 3.2 25.6 + - + +
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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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576A LEU* 3.9 19.3 - - + -
577A LEU* 3.3 27.1 - - + -
615A ASP 3.0 14.1 + - - +
616A ASP 3.7 7.4 - - - +
618A HIS* 1.3 77.1 - - - +
620A ALA* 1.3 61.8 + - - +
622A ILE* 3.5 11.5 + - + +
623A ILE* 3.2 24.3 + - + +
629A LEU* 4.3 12.6 - - + -
643A PHE* 3.3 43.3 - - + -
644A PHE* 3.9 22.9 - - + -
650A LEU* 4.3 8.7 - - + -
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Residues in contact with ALA 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 ASP 3.2 6.9 + - - +
617A ASP* 3.2 10.9 + - - +
618A HIS 3.1 0.6 - - - -
619A ILE* 1.3 76.2 - - - +
621A GLN* 1.3 59.7 + - + +
623A ILE* 3.0 7.5 + - - +
624A GLU* 2.8 28.9 + - - +
650A LEU* 3.7 24.5 - - + -
653A ILE* 4.3 12.3 - - + -
656A LEU* 3.8 20.7 - - + +
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Residues in contact with GLN 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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603A LEU 5.4 0.2 + - - -
604A PHE* 3.8 19.8 - - + +
605A GLU* 3.5 43.4 - - - +
617A ASP* 3.1 18.0 + - + +
618A HIS* 3.5 30.5 + - - +
620A ALA* 1.3 76.7 - - + +
622A ILE* 1.3 61.4 + - - +
624A GLU* 3.4 12.0 + - - +
625A LEU* 3.1 23.9 + - - +
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Residues in contact with ILE 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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571A ARG 4.9 0.7 - - - +
573A PRO* 4.4 12.6 - - + -
576A LEU* 3.6 31.0 - - + -
588A TRP* 4.0 22.2 - - + -
604A PHE* 3.7 26.5 - - + -
618A HIS* 3.2 17.6 + - + +
619A ILE* 3.6 10.8 - - + +
620A ALA 3.1 0.2 - - - -
621A GLN* 1.3 76.5 - - - +
623A ILE* 1.3 53.1 + - - +
625A LEU* 3.2 1.6 + - - +
626A LEU* 2.7 35.4 + - + +
629A LEU* 4.5 10.1 - - + -
689A LEU* 3.5 31.6 - - + -
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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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619A ILE* 3.2 19.7 + - + +
620A ALA* 3.0 11.3 + - - +
622A ILE* 1.3 78.0 - - - +
624A GLU* 1.3 59.3 + - - +
627A GLY* 2.6 53.1 + - - +
628A GLU* 3.4 22.9 - - - +
629A LEU* 3.0 39.5 - - + +
644A PHE* 5.6 7.2 - - + -
650A LEU* 5.7 3.6 - - + -
656A LEU* 4.3 20.2 - - + -
658A PHE* 3.6 15.5 - - + -
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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 ALA 2.8 19.0 + - - +
621A GLN* 3.7 11.6 - - - +
622A ILE 3.3 0.2 - - - -
623A ILE* 1.3 73.3 - - - +
625A LEU* 1.3 61.5 + - + +
656A LEU* 5.4 5.4 - - + +
657A LYS* 2.7 35.8 + - - +
658A PHE* 3.3 12.1 - - - +
659A TRP* 2.8 44.8 + - + +
660A PRO 4.5 0.2 - - - -
657B LYS* 3.8 22.3 - - - +
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Residues in contact with LEU 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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603A LEU* 4.1 25.6 - - + +
604A PHE* 3.8 28.7 - - + -
621A GLN 3.1 15.8 + - - +
622A ILE 3.9 1.6 - - - +
624A GLU* 1.3 81.0 - - + +
626A LEU* 1.3 74.1 + - + +
659A TRP 3.4 20.2 - - - +
660A PRO* 4.0 14.4 - - - +
661A LEU* 3.6 32.4 + - + +
664A VAL* 4.1 10.1 - - + -
687A LEU* 4.4 8.1 - - + -
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Residues in contact with LEU 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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588A TRP* 3.6 25.8 - - + -
604A PHE* 5.1 0.2 - - + -
622A ILE* 2.7 18.4 + - + +
625A LEU* 1.3 95.5 - - + +
627A GLY* 1.3 58.8 + - - +
628A GLU 4.8 0.2 - - - +
661A LEU* 5.9 3.6 - - + -
684A SER* 5.6 7.0 - - - +
687A LEU* 3.0 49.1 - - + +
689A LEU* 3.8 25.6 - - + +
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Residues in contact with GLY 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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623A ILE* 2.6 46.3 + - - +
624A GLU 4.6 0.2 - - - -
625A LEU 3.7 0.8 - - - -
626A LEU* 1.3 74.9 - - - +
628A GLU* 1.3 68.4 + - - +
629A LEU* 4.3 0.2 - - - +
658A PHE* 4.4 11.8 - - - -
689A LEU* 3.8 5.4 - - - +
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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