Contacts of the helix formed by residues 632 - 648 (chain A) in PDB entry 2YD0
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 SER 632 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A GLY* 4.7 3.8 - - - -
631A VAL* 1.3 80.3 - - - +
633A SER* 1.3 55.5 + - - +
634A ASN* 3.5 8.2 + - - +
635A ASP* 2.9 33.8 + - - -
636A ARG* 2.8 37.2 + - - +
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Residues in contact with SER 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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632A SER* 1.3 73.3 - - - +
634A ASN* 1.3 64.7 + - - +
636A ARG* 3.2 24.4 + - - +
637A ALA* 2.9 28.1 + - - +
669A GLU* 3.5 26.7 + - - +
671A MET* 5.1 2.0 - - - -
672A PRO* 3.7 20.4 - - - +
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Residues in contact with ASN 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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397A GLY 4.1 10.5 + - - -
398A ASP* 3.3 31.7 + - - +
401A PHE* 4.4 14.8 - - + +
603A GLY* 3.8 31.3 + - - +
604A MET* 4.5 5.2 - - + +
632A SER* 3.2 8.2 + - - +
633A SER* 1.3 83.6 - - - +
635A ASP* 1.3 62.1 + - - +
637A ALA* 3.3 7.6 + - - +
638A SER* 3.1 23.2 + - - -
671A MET* 3.8 15.9 - - - +
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Residues in contact with ASP 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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570A ILE* 4.4 7.3 - - - +
599A LYS* 3.2 28.0 + - - -
601A ASN 3.6 0.2 - - - +
602A VAL* 3.5 11.6 - - - +
603A GLY* 2.8 28.5 + - - -
604A MET 4.2 0.2 + - - -
631A VAL* 3.7 18.9 - - + +
632A SER* 2.9 32.1 + - - +
634A ASN* 1.3 71.9 - - - +
636A ARG* 1.3 65.8 + - - +
638A SER* 2.8 21.5 + - - -
639A LEU* 3.1 14.5 + - - +
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Residues in contact with ARG 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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624A LEU* 3.6 23.5 - - + +
628A HIS* 3.5 33.5 + - - -
629A THR* 4.1 16.2 - - - +
631A VAL* 3.3 15.4 + - + -
632A SER* 2.8 12.5 + - - +
633A SER* 3.2 41.8 + - - +
635A ASP* 1.3 78.0 - - - +
637A ALA* 1.3 62.6 + - - +
638A SER 3.3 0.2 + - - -
639A LEU* 3.3 9.5 + - - +
640A ILE* 3.2 27.3 + - - +
663A TYR* 3.5 17.2 - - + +
667A GLU* 2.9 39.2 + - - -
669A GLU* 3.9 11.1 - - - +
672A PRO* 4.2 2.0 - - + -
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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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401A PHE* 6.0 1.8 - - + -
405A PHE* 4.3 8.0 - - + -
633A SER 2.9 14.4 + - - +
634A ASN* 3.5 8.7 - - - +
635A ASP 3.3 0.4 - - - -
636A ARG* 1.3 76.6 - - - +
638A SER* 1.3 57.2 + - - +
640A ILE* 3.4 5.0 + - - +
641A ASN* 3.1 22.7 + - - +
671A MET* 4.1 15.5 - - + +
672A PRO* 4.0 25.1 - - + +
675A GLN* 3.4 21.8 - - + +
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Residues in contact with SER 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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405A PHE* 3.8 11.6 - - - -
599A LYS* 3.3 22.8 + - - -
601A ASN* 5.9 1.6 - - - -
604A MET* 3.4 33.2 - - - -
634A ASN 3.1 9.2 + - - -
635A ASP* 2.8 18.4 + - - -
637A ALA* 1.3 75.4 - - - +
639A LEU* 1.3 58.8 + - - +
642A ASN* 2.9 42.2 + - - -
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Residues in contact with LEU 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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599A LYS* 3.7 30.3 - - + -
612A TYR* 4.5 4.9 - - + -
617A TRP* 3.8 23.1 - - + -
620A LEU* 4.0 35.0 - - + +
623A LEU* 6.4 0.9 - - + -
624A LEU* 3.9 37.5 - - + -
631A VAL* 4.9 6.7 - - + -
635A ASP 3.1 15.1 + - - +
636A ARG* 3.6 8.3 - - - +
638A SER* 1.3 80.2 + - - +
640A ILE* 1.3 63.8 + - - +
642A ASN* 4.7 0.7 - - + -
643A ALA* 3.0 26.5 + - - +
660A LEU* 4.9 3.1 - - + -
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Residues in contact with ILE 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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636A ARG 3.2 15.4 + - - +
637A ALA* 3.6 7.4 - - - +
638A SER 3.3 0.2 - - - -
639A LEU* 1.3 79.5 - - - +
641A ASN* 1.3 64.8 + - - +
643A ALA* 3.4 1.8 + - - +
644A PHE* 3.1 44.6 + - + -
660A LEU* 4.2 16.4 - - + -
661A SER* 5.5 2.0 - - - +
663A TYR* 3.8 33.2 - - + +
664A LEU* 3.9 11.2 - - + -
672A PRO* 3.6 28.7 - - + +
675A GLN* 4.4 1.8 - - + -
676A GLY* 4.0 23.1 - - - +
679A GLU* 4.2 5.2 - - + -
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Residues in contact with ASN 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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405A PHE* 3.4 37.5 + - + +
637A ALA 3.1 12.2 + - - +
638A SER 4.0 0.7 - - - +
640A ILE* 1.3 79.4 - - - +
642A ASN* 1.3 69.9 + - - +
644A PHE* 3.2 4.3 + - - +
645A GLN* 2.9 57.0 + - - +
675A GLN* 3.6 16.3 - - - +
679A GLU* 2.9 29.7 + - - +
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Residues in contact with ASN 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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405A PHE* 4.4 6.7 - - - -
601A ASN* 5.5 1.9 + - - +
604A MET* 5.9 1.6 - - - -
608A TYR 4.6 1.7 + - - +
609A ILE* 3.5 26.8 - - + +
610A VAL* 3.0 41.3 + - - +
617A TRP* 4.2 6.3 - - + -
638A SER* 2.9 27.4 + - - +
639A LEU* 4.1 2.2 - - - +
641A ASN* 1.3 84.8 + - - +
643A ALA* 1.3 67.2 + - - +
645A GLN* 3.8 4.8 - - - +
646A LEU* 2.9 32.1 + - + +
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Residues in contact with ALA 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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617A TRP* 3.9 13.1 - - + -
639A LEU 3.0 18.5 + - - +
640A ILE* 3.5 5.8 - - - +
642A ASN* 1.3 76.9 - - - +
644A PHE* 1.3 63.8 + - + +
646A LEU* 3.4 0.5 + - - +
647A VAL* 3.2 23.6 + - - +
652A LEU* 3.6 27.6 - - + +
657A ALA* 4.1 13.2 - - + -
660A LEU* 4.3 13.2 - - + -
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Residues in contact with PHE 644 (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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640A ILE* 3.1 36.2 + - + -
641A ASN 3.2 4.6 + - - +
643A ALA* 1.3 73.2 - - + +
645A GLN* 1.3 67.1 + - - +
646A LEU 3.1 1.3 - - - -
647A VAL* 3.1 16.6 + - + +
648A SER* 3.2 13.0 + - - -
654A ILE* 4.0 8.7 - - + -
657A ALA* 3.6 31.6 - - + -
658A LEU* 3.9 16.2 - - + -
660A LEU* 6.0 1.1 - - + -
661A SER* 3.5 25.8 - - - -
679A GLU* 3.6 37.9 - - + +
680A LEU* 4.2 8.5 - - + -
683A MET* 3.7 28.3 - - + -
921A TRP* 5.7 0.2 + - - -
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Residues in contact with GLN 645 (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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405A PHE 5.5 0.2 + - - -
408A MET* 3.7 38.8 - - - +
409A GLU* 5.8 0.2 - - - -
412A ALA* 4.7 1.4 - - - +
530A PHE* 3.9 8.2 - - - -
549A TYR* 2.5 47.1 + - - +
551A LYS* 4.8 7.2 - - - +
609A ILE* 3.8 22.0 - - + +
641A ASN* 2.9 48.1 + - - +
642A ASN* 3.2 4.0 + - - +
644A PHE* 1.3 76.7 - - - +
646A LEU* 1.3 60.3 + - - +
648A SER* 3.3 13.6 + - - -
649A ILE 3.8 0.9 + - - -
679A GLU* 5.6 2.7 - - - +
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Residues in contact with LEU 646 (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 LEU* 3.5 35.7 - - + -
609A ILE* 4.0 10.5 - - + -
610A VAL 3.6 9.9 - - - +
611A HIS* 3.7 22.9 - - + +
617A TRP* 3.5 31.2 - - + +
642A ASN 2.9 24.2 + - - +
643A ALA* 3.8 5.2 - - - +
644A PHE 3.1 0.2 - - - -
645A GLN* 1.3 75.2 - - - +
647A VAL* 1.3 62.8 + - - +
648A SER 3.1 1.8 - - - -
649A ILE* 3.5 8.5 + - + +
650A GLY 3.3 3.8 + - - -
651A LYS* 3.0 39.1 + - + -
652A LEU* 3.4 12.9 + - + -
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Residues in contact with VAL 647 (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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643A ALA 3.2 16.5 + - - +
644A PHE* 3.1 13.2 + - + +
646A LEU* 1.3 75.3 - - - +
648A SER* 1.3 61.5 + - - +
649A ILE 3.2 1.2 + - - -
650A GLY* 3.2 12.0 + - - -
652A LEU* 3.4 15.8 - - + +
653A SER 4.1 1.1 - - - +
654A ILE* 3.8 44.9 - - + +
657A ALA* 3.7 22.9 - - + -
921A TRP* 4.0 18.0 - - - +
924A LYS* 4.9 7.7 + - + +
925A ASN* 4.2 9.2 + - - +
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Residues in contact with SER 648 (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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549A TYR* 4.0 0.9 - - - -
551A LYS* 3.7 34.3 + - - +
644A PHE 3.2 13.0 + - - -
645A GLN* 3.5 10.1 + - - -
646A LEU 3.1 1.0 - - - -
647A VAL* 1.3 77.6 - - - +
649A ILE* 1.3 59.9 + - - +
650A GLY 3.6 0.4 - - - -
917A GLU* 3.5 25.9 - - - +
921A TRP* 4.3 17.7 + - - -
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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