Contacts of the helix formed by residues 612 - 627 (chain A) in PDB entry 1Q2L
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 ARG 612 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ASN* 6.1 0.4 - - - +
505A PRO 3.5 19.2 + - - +
506A TYR* 3.9 31.4 - - + +
507A ILE 3.0 27.1 + - - +
508A PRO* 4.3 7.6 - - + +
509A ASP* 3.3 27.9 + - - -
592A ILE* 4.3 8.1 - - + -
609A TYR* 4.4 1.8 + - - +
610A THR 3.3 0.4 - - - -
611A GLN* 1.3 101.9 + - - +
613A LEU* 1.3 66.3 + - - +
614A PRO* 3.4 2.7 - - - -
615A GLN* 3.2 18.8 + - - +
616A LEU* 2.9 20.4 + - - +
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Residues in contact with LEU 613 (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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548A ALA* 3.8 32.8 - - + +
550A VAL* 3.7 28.9 - - + +
592A ILE* 4.0 27.3 - - + +
606A ALA* 4.1 29.2 - - + -
607A ASN 4.7 0.7 - - - +
608A GLY 4.2 7.0 - - - +
609A TYR 3.7 9.8 + - - +
610A THR* 3.2 10.7 + - - +
612A ARG* 1.3 76.2 - - - +
614A PRO* 1.3 73.8 - - + +
616A LEU* 3.0 4.4 + - + +
617A PHE* 2.7 27.5 + - + +
708A MET* 4.2 6.5 - - - -
716A LEU* 5.6 0.4 - - + -
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Residues in contact with PRO 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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610A THR* 3.4 11.4 - - - +
611A GLN 4.1 5.6 - - - +
612A ARG 3.6 2.7 - - - -
613A LEU* 1.3 94.2 - - + +
615A GLN* 1.3 62.3 + - - +
617A PHE* 3.2 1.7 + - - +
618A GLN* 3.0 35.7 + - - +
708A MET* 4.2 22.9 - - + -
712A GLN* 5.9 2.7 - - + +
716A LEU* 3.8 24.7 - - + -
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Residues in contact with GLN 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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505A PRO* 4.2 26.0 - - - +
506A TYR* 3.7 26.3 + - + +
612A ARG* 3.2 20.2 + - - +
614A PRO* 1.3 79.6 - - - +
616A LEU* 1.3 61.8 + - - +
618A GLN* 3.4 9.4 + - - +
619A ALA* 3.0 23.8 + - + +
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Residues in contact with LEU 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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506A TYR* 3.6 20.6 - - + -
583A LEU* 3.7 34.5 - - + -
587A ALA* 4.0 17.3 - - + -
592A ILE* 3.8 35.9 - - + -
594A PHE* 3.9 16.4 - - + -
606A ALA* 4.4 12.6 - - + -
612A ARG 2.9 12.7 + - - +
613A LEU* 3.5 8.3 - - + +
615A GLN* 1.3 75.4 - - - +
617A PHE* 1.3 70.6 + - - +
619A ALA 3.2 1.2 + - - -
620A LEU* 2.9 24.5 + - + +
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Residues in contact with PHE 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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550A VAL* 3.6 45.1 - - + -
552A LEU* 3.7 33.0 - - + -
604A VAL* 3.9 24.2 - - + -
606A ALA* 3.7 25.1 - - + -
613A LEU* 2.7 20.6 + - + +
614A PRO 3.6 4.0 - - - +
616A LEU* 1.3 77.2 - - + +
618A GLN* 1.3 61.7 + - - +
620A LEU* 3.3 5.4 - - + +
621A LEU* 3.1 45.1 + - + +
702A PHE* 4.2 7.2 - + - -
716A LEU* 4.3 13.7 - - + -
720A VAL* 4.1 15.7 - - + -
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Residues in contact with GLN 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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614A PRO* 3.0 25.4 + - - +
615A GLN* 3.9 7.3 - - - +
616A LEU 3.2 0.2 - - - -
617A PHE* 1.3 75.9 - - - +
619A ALA* 1.3 58.7 + - - +
621A LEU* 3.6 1.2 + - - -
622A GLU* 3.0 13.5 + - - +
716A LEU* 4.0 16.2 - - + +
719A ASP* 3.7 37.9 + - - +
720A VAL* 4.5 3.6 - - + -
722A LYS* 5.4 2.9 + - - -
723A GLN* 2.7 47.6 + - - +
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Residues in contact with ALA 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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506A TYR* 3.3 26.9 - - - +
580A LEU* 4.3 0.2 - - - +
583A LEU* 3.9 16.9 - - + +
615A GLN* 3.0 12.5 + - + +
616A LEU 3.8 3.1 - - - +
618A GLN* 1.3 74.5 - - - +
620A LEU* 1.3 61.4 + - - +
622A GLU* 3.6 7.3 - - - +
623A GLY* 2.9 26.9 + - - -
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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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580A LEU* 3.6 19.9 - - + +
583A LEU* 3.5 12.1 - - + +
594A PHE* 3.6 53.8 - - + -
596A THR* 4.5 11.2 - - + -
604A VAL* 3.5 31.6 - - + -
605A ASN 4.8 0.2 - - - +
616A LEU* 2.9 18.7 + - + +
617A PHE* 3.3 15.3 - - + +
618A GLN 3.2 0.2 - - - -
619A ALA* 1.3 78.6 - - - +
621A LEU* 1.3 67.3 + - + +
623A GLY 3.2 0.2 + - - -
624A TYR* 3.0 21.5 + - + +
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Residues in contact with LEU 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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552A LEU* 4.0 17.0 - - + -
554A LEU* 4.8 0.4 - - + -
602A LEU* 4.3 2.2 - - + -
604A VAL* 3.9 35.2 - - + -
617A PHE* 3.1 42.2 + - + +
618A GLN 4.1 3.4 - - - +
620A LEU* 1.3 80.6 - - + +
622A GLU* 1.3 61.7 + - - +
624A TYR* 4.2 4.5 - - + -
625A PHE* 3.1 53.2 + - + +
720A VAL* 4.5 9.9 - - + -
723A GLN* 4.0 10.8 - - - +
724A LEU* 4.2 15.7 - - + +
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Residues in contact with GLU 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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618A GLN 3.0 20.0 + - - +
619A ALA* 3.6 8.5 - - - +
621A LEU* 1.3 79.3 - - - +
623A GLY* 1.3 62.0 + - - +
625A PHE* 3.5 1.8 + - - +
626A SER* 2.5 61.6 + - - +
723A GLN* 3.2 15.2 + - + +
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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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576A ALA* 4.9 0.2 - - - +
579A ALA* 4.6 4.8 - - - +
580A LEU* 3.9 16.5 - - - +
619A ALA 2.9 16.4 + - - -
620A LEU 3.8 1.1 - - - -
622A GLU* 1.3 82.6 + - - +
624A TYR* 1.3 61.7 + - - +
626A SER* 4.3 1.6 - - - -
627A TYR* 3.3 29.4 + - - +
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Residues in contact with TYR 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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569A PHE* 4.1 8.5 + - - -
572A ASN* 3.5 21.3 + - - -
573A ASP* 2.8 40.6 + - - +
576A ALA* 3.4 27.4 - - + -
580A LEU* 4.0 9.3 - - + +
596A THR* 3.8 25.8 - - + -
602A LEU* 3.4 31.5 - - + +
604A VAL* 5.9 0.7 - - + -
620A LEU* 3.0 16.8 + - + +
621A LEU* 3.6 9.9 - - + +
622A GLU 3.2 0.2 - - - -
623A GLY* 1.3 78.3 - - - +
625A PHE* 1.3 76.9 + + + +
627A TYR* 3.2 20.1 - - - -
691A ARG* 3.5 6.4 - - - -
694A LEU* 4.2 8.7 - - + -
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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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554A LEU* 3.9 6.5 - - + -
602A LEU* 3.6 33.0 - - + -
621A LEU* 3.1 39.3 + - + +
622A GLU* 3.9 1.8 - - - +
624A TYR* 1.3 88.1 - + - +
626A SER* 1.3 59.8 + - - +
691A ARG* 3.4 56.3 + - + +
692A ASP* 5.0 3.7 - - - +
694A LEU* 4.0 15.9 - - + -
695A LYS* 3.6 44.0 - - + -
724A LEU* 3.7 17.9 - - + -
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Residues in contact with SER 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 GLU* 2.5 39.2 + - - -
623A GLY* 4.2 1.7 - - - -
625A PHE* 1.3 80.1 - - - +
627A TYR* 1.3 70.0 + - - +
628A THR* 4.4 4.0 + - - -
691A ARG* 3.9 5.6 - - - +
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Residues in contact with TYR 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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572A ASN* 2.7 40.6 + - - -
575A LEU* 3.5 50.1 - - + +
576A ALA* 3.9 9.9 - - - -
579A ALA* 3.5 22.4 - - + -
623A GLY* 3.3 16.4 + - - +
624A TYR 3.2 20.2 - - - -
626A SER* 1.3 82.4 - - - +
628A THR* 1.3 73.5 + - - +
629A ALA* 4.0 10.1 - - + -
687A VAL* 4.0 5.2 - - - +
688A LEU* 4.5 10.5 - - + +
691A ARG* 2.8 43.3 + - - +
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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