Contacts of the helix formed by residues 632 - 643 (chain A) in PDB entry 2QTL
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 HIS 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A TRP* 4.0 19.3 - + + -
577A PHE* 4.4 5.8 - - + -
606A LYS* 3.5 41.5 + - + +
628A ASN* 3.1 28.9 + - - +
629A ILE 3.0 9.2 + - - +
631A LEU* 1.3 91.6 + - + +
633A GLY* 1.3 64.7 + - - +
634A GLN* 3.2 4.1 + - - -
635A GLN* 3.3 28.0 + - - +
636A VAL* 3.1 21.2 + - + +
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Residues in contact with GLY 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 ILE 3.2 9.6 + - - -
630A GLN 3.3 8.8 + - - -
631A LEU 3.5 1.2 - - - -
632A HIS* 1.3 77.9 - - - +
634A GLN* 1.3 57.0 + - - +
636A VAL* 4.3 1.8 - - - -
637A ALA* 2.8 29.1 + - - +
667A ILE* 3.3 32.7 - - - +
671A GLU* 3.9 5.2 - - - -
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Residues in contact with GLN 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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632A HIS 3.2 1.0 - - - -
633A GLY* 1.3 76.3 - - - +
635A GLN* 1.3 67.6 + - + +
637A ALA* 3.9 1.7 - - - +
638A ARG* 3.1 53.7 + - + +
671A GLU* 3.6 31.1 + - - +
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Residues in contact with GLN 635 (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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575A TRP* 3.4 36.5 - - + -
604A HIS* 4.6 9.9 + - - -
632A HIS* 3.3 34.8 + - - +
634A GLN* 1.3 83.1 - - + +
636A VAL* 1.3 59.5 + - - +
638A ARG* 3.4 27.9 + - - +
639A ILE* 2.9 38.0 + - + +
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Residues in contact with VAL 636 (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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541A ILE* 4.0 27.8 - - + -
575A TRP* 5.5 3.4 - - + -
577A PHE* 4.2 25.8 - - + -
629A ILE* 4.2 14.4 - - + -
632A HIS* 3.1 21.5 + - + +
633A GLY* 3.7 6.5 - - - +
635A GLN* 1.3 78.5 - - + +
637A ALA* 1.3 62.4 + - - +
639A ILE* 3.7 1.6 - - - +
640A LEU* 3.1 31.2 + - + +
647A ILE* 5.0 1.1 - - + -
664A LEU* 3.8 28.9 - - + -
667A ILE* 4.6 6.7 - - + -
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Residues in contact with ALA 637 (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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633A GLY 2.8 20.5 + - - +
634A GLN 3.9 1.6 - - - +
636A VAL* 1.3 74.8 - - - +
638A ARG* 1.3 53.5 + - - +
640A LEU* 3.3 3.0 + - - -
641A LEU* 2.8 56.2 + - + +
642A GLN* 4.5 2.7 - - - +
667A ILE* 4.2 8.3 - - + +
668A ILE* 5.2 5.4 - - + -
671A GLU* 3.7 27.1 - - + -
672A VAL* 5.2 0.9 - - + -
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Residues in contact with ARG 638 (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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634A GLN* 3.1 56.0 + - - +
635A GLN* 3.7 29.2 - - - +
637A ALA* 1.3 73.6 - - - +
639A ILE* 1.3 61.6 + - + +
642A GLN* 2.8 58.4 + - + +
643A GLU* 3.1 29.7 + - - +
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Residues in contact with ILE 639 (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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539A PRO* 4.1 21.5 - - + +
540A ILE* 5.0 0.7 - - - +
541A ILE* 3.8 28.3 - - + -
573A ALA* 5.2 2.0 - - + -
575A TRP* 3.3 42.6 - - + +
635A GLN* 2.9 23.6 + - + +
636A VAL* 3.7 3.6 - - - +
638A ARG* 1.3 78.5 - - + +
640A LEU* 1.3 63.0 + - + +
643A GLU* 3.4 29.3 + - - +
644A ASN 3.4 0.2 + - - -
645A GLY* 2.9 37.9 + - - -
646A HIS 4.8 0.4 - - - +
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Residues in contact with LEU 640 (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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541A ILE* 4.2 8.7 - - + -
636A VAL* 3.1 34.3 + - + +
637A ALA* 4.0 4.0 - - - +
639A ILE* 1.3 76.9 - - + +
641A LEU* 1.3 69.7 + - + +
644A ASN 4.3 2.0 + - - -
645A GLY 3.6 26.6 + - - +
646A HIS* 3.9 6.3 - - - -
647A ILE* 3.9 35.4 - - + +
664A LEU* 4.5 9.2 - - + -
668A ILE* 5.6 5.4 - - + -
683A LEU* 5.2 3.8 - - + -
686A LEU* 4.2 24.9 - - + +
691A ARG* 2.9 31.3 + - - +
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Residues in contact with LEU 641 (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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637A ALA* 2.8 28.5 + - + +
640A LEU* 1.3 88.1 - - + +
642A GLN* 1.3 69.3 + - + +
643A GLU 3.8 0.2 - - - -
644A ASN 5.0 0.4 - - - -
668A ILE* 4.3 23.8 - - + -
672A VAL* 3.8 28.7 - - + -
682A THR* 3.8 26.5 - - + -
686A LEU* 4.6 9.9 - - + -
691A ARG* 5.7 0.9 - - - +
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Residues in contact with GLN 642 (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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637A ALA* 4.3 4.8 + - - +
638A ARG* 2.8 54.9 + - + +
641A LEU* 1.3 82.7 - - - +
643A GLU* 1.3 64.0 + - + +
644A ASN* 3.7 8.3 + - - -
672A VAL* 6.3 1.4 - - - +
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Residues in contact with GLU 643 (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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538A ILE* 4.4 2.3 - - - +
539A PRO* 3.4 29.5 - - + +
638A ARG* 3.1 36.4 + - - +
639A ILE* 3.4 30.1 + - - +
642A GLN* 1.3 84.3 - - + +
644A ASN* 1.3 77.9 + - - +
645A GLY 3.2 2.3 + - - -
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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