Contacts of the helix formed by residues 627 - 639 (chain A) in PDB entry 5A7R
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 GLN 627 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A MET 4.0 0.6 + - - -
626A SER* 1.3 71.6 - - - +
628A GLU* 1.3 57.0 + - - +
630A ILE* 3.3 10.5 + - - +
631A ALA* 2.9 27.5 + - - +
682A TYR* 4.6 0.9 + - - -
691A PRO* 3.6 23.4 - - + +
692A THR 3.9 0.9 + - - -
693A GLY* 2.9 48.0 + - - +
694A LEU 4.8 0.7 - - - -
695A VAL* 4.0 12.1 - - + -
764A GLU* 3.0 41.1 + - - +
785A GLY 4.5 6.9 + - - -
787A GLU* 3.1 31.4 + - - +
789A TYR* 3.5 3.2 + - - -
811A ARG* 4.8 5.7 + - - -
817A ARG* 5.0 3.3 + - - +
1979A GOL 5.4 0.2 - - - -
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Residues in contact with GLU 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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494A VAL* 3.2 30.4 - - + +
495A PRO* 4.3 5.6 - - + +
497A PRO* 5.6 4.7 - - - +
600A ILE* 4.5 14.6 - - + +
607A ILE* 4.2 23.1 - - + +
626A SER* 3.1 10.1 + - - +
627A GLN* 1.3 75.6 - - - +
629A GLN* 1.3 64.8 + - - +
631A ALA* 3.2 6.2 + - - +
632A SER* 3.1 22.2 + - - -
690A ALA* 4.0 18.0 - - + +
691A PRO* 3.9 24.0 + - + +
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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
----------------------------------------------------------
483A THR* 2.7 49.7 + - - -
484A ILE* 3.6 8.8 - - - +
497A PRO* 4.1 7.3 - - + +
607A ILE* 3.0 42.8 + - + +
608A CYS* 3.8 18.5 - - - +
609A THR 4.9 1.2 - - - +
625A MET* 3.5 8.1 - - + +
626A SER* 2.9 40.6 + - - +
628A GLU* 1.3 74.3 - - + +
630A ILE* 1.3 63.6 + - - +
632A SER* 3.3 4.3 + - - -
633A LEU* 3.1 27.3 + - - +
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Residues in contact with ILE 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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625A MET* 3.6 29.4 - - + -
626A SER 3.0 18.6 + - - +
627A GLN* 3.6 10.1 - - - +
629A GLN* 1.3 76.4 - - - +
631A ALA* 1.3 56.6 + - - +
633A LEU* 3.2 5.4 + - - +
634A LEU* 2.9 48.8 + - + +
682A TYR* 4.2 0.2 - - - +
695A VAL* 3.7 35.0 - - + -
697A PHE* 4.1 12.3 - - + -
764A GLU* 3.8 22.4 - - + -
767A ILE* 3.9 17.3 - - + -
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Residues in contact with ALA 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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600A ILE* 4.0 16.1 - - + +
627A GLN 2.9 12.6 + - - +
628A GLU* 3.2 11.0 + - - +
630A ILE* 1.3 76.2 - - - +
632A SER* 1.3 57.0 + - - +
634A LEU* 3.4 2.2 + - - +
635A ALA* 3.0 30.3 + - - +
682A TYR* 3.3 21.2 + - - +
683A PHE* 4.5 2.9 - - - -
686A VAL* 3.7 26.9 - - + -
691A PRO* 5.2 1.3 - - + -
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Residues in contact with SER 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ILE* 2.8 34.5 + - - +
601A ALA* 4.0 0.5 + - - -
604A LEU* 3.5 26.0 + - - +
607A ILE* 4.0 21.5 - - - +
628A GLU 3.1 12.6 + - - -
629A GLN 3.3 7.8 + - - -
631A ALA* 1.3 75.0 - - - +
633A LEU* 1.3 61.2 + - - +
635A ALA* 3.4 3.6 + - - +
636A ASN* 3.0 29.7 + - - -
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Residues in contact with LEU 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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513A MET* 4.1 14.1 - - + -
604A LEU* 3.7 19.5 - - + -
608A CYS* 3.7 15.0 - - - -
612A ILE* 4.1 9.4 - - + -
625A MET* 3.4 33.9 - - + -
629A GLN 3.1 15.2 + - - +
630A ILE* 3.7 5.4 - - - +
632A SER* 1.3 76.2 - - - +
634A LEU* 1.3 56.4 + - - +
636A ASN* 3.2 3.8 + - - +
637A ALA* 3.0 21.8 + - - +
642A PHE* 3.4 31.0 - - + -
767A ILE* 3.7 24.0 - - + -
770A LEU* 4.1 9.9 - - + -
771A PHE* 5.9 0.2 - - + -
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Residues in contact with LEU 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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630A ILE* 2.9 29.7 + - + +
631A ALA 4.0 2.9 - - - +
633A LEU* 1.3 72.8 - - - +
635A ALA* 1.3 61.9 + - - +
637A ALA* 3.2 6.6 + - + +
638A PHE 2.9 23.0 + - - -
659A ILE* 4.9 0.2 - - + -
661A PHE* 4.3 12.8 - - + -
682A TYR* 3.6 30.5 - - + +
683A PHE* 3.6 21.9 - - + -
763A PRO* 3.4 23.8 - - + +
766A ILE* 3.8 31.4 - - + -
767A ILE* 3.9 20.0 - - + +
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Residues in contact with ALA 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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597A MET* 3.6 31.4 - - + +
600A ILE* 3.8 12.3 - - + -
601A ALA* 3.8 6.5 - - + -
631A ALA 3.0 17.6 + - - +
632A SER 3.8 4.7 - - - +
633A LEU 3.3 0.4 - - - -
634A LEU* 1.3 74.4 - - - +
636A ASN* 1.3 63.4 + - - +
638A PHE* 3.3 4.6 + - - +
639A PHE* 3.1 28.9 + - - -
683A PHE* 3.7 15.6 - - + -
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Residues in contact with ASN 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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514A PRO* 3.8 6.0 - - - +
536A TRP* 3.9 10.7 - - - -
539A ILE* 5.4 0.5 - - - +
601A ALA* 3.1 32.3 + - - +
602A LEU* 5.8 0.3 - - - +
604A LEU* 3.7 21.1 - - - +
632A SER 3.0 26.3 + - - -
633A LEU 3.2 8.9 + - - +
635A ALA* 1.3 73.2 - - - +
637A ALA* 1.3 65.5 + - - +
639A PHE* 3.2 3.2 + - - -
640A CYS 3.0 17.8 + - - -
641A THR* 2.7 42.3 + - - +
642A PHE* 3.8 13.0 - - + -
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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 LEU 3.0 13.7 + - - +
634A LEU* 3.2 12.1 + - + +
636A ASN* 1.3 75.4 - - - +
638A PHE* 1.3 63.5 + - - +
640A CYS* 3.0 9.0 + - - -
642A PHE* 3.5 16.5 - - + -
659A ILE* 3.4 31.0 - - + +
660A ASN* 3.6 2.9 - - - -
661A PHE* 2.9 36.0 + - + -
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Residues in contact with PHE 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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553A LEU* 4.3 14.1 - - + -
557A ILE* 4.4 1.5 - - + +
573A LEU* 5.1 1.6 - - + -
594A LEU* 4.0 11.0 - - + -
597A MET* 3.6 26.2 - - + -
634A LEU 2.9 13.2 + - - +
635A ALA 3.5 8.5 - - - +
637A ALA* 1.3 77.8 - - - +
639A PHE* 1.3 83.9 + + - +
640A CYS* 3.2 8.9 + - - -
661A PHE* 3.7 26.5 - + + +
665A PHE* 3.6 43.7 - + - -
676A LEU* 5.1 5.2 - - + -
679A LEU* 6.2 2.0 - - + -
680A PHE* 3.7 35.7 - + - -
683A PHE* 4.1 9.4 - + + -
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Residues in contact with PHE 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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543A LEU* 3.8 26.5 - - + -
547A PHE* 4.9 1.6 - + - -
553A LEU* 3.8 21.5 - - + -
557A ILE* 3.8 10.3 - - + +
560A TYR* 2.5 33.5 + - - +
594A LEU* 4.1 10.5 - - + -
597A MET* 3.7 19.7 - - + -
598A VAL* 3.6 45.5 - - + -
601A ALA* 4.3 9.6 - - + -
635A ALA 3.1 25.8 + - - +
636A ASN* 3.2 4.2 + - - +
638A PHE* 1.3 100.1 - + - +
640A CYS* 1.3 68.7 + - - +
641A THR* 3.4 5.8 - - + -
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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