Contacts of the helix formed by residues 622 - 640 (chain A) in PDB entry 3E0D
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 LEU 622 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASP* 3.5 37.7 - - + +
468A PHE 3.1 13.5 + - - +
470A ASP* 3.4 11.6 + - - +
620A LEU* 3.5 1.1 + - + -
621A GLY* 1.1 76.0 - - - +
623A ARG* 1.3 65.6 + - - +
624A THR* 3.7 11.4 - - - +
625A LEU* 3.5 21.9 + - + +
626A THR 3.6 4.9 + - - -
668A PHE* 4.2 9.2 - - + -
821A TYR* 4.4 11.2 - - + +
824A LEU* 3.9 25.6 - - + -
7C G 5.7 2.9 - - - +
8C T 2.0 60.3 - - - +
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Residues in contact with ARG 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ASP* 3.4 26.4 + - - -
622A LEU 1.3 65.7 - - - -
624A THR* 1.3 61.4 + - - +
626A THR* 2.9 15.0 + - - +
627A PHE* 2.9 20.3 + - - +
846A VAL* 2.8 51.9 + - + +
847A GLU* 4.9 13.6 - - - +
848A ARG* 5.7 5.5 - - - +
849A HIS* 4.6 19.2 - - - +
7C G 3.9 0.7 - - - +
8C T 2.1 74.3 + - + +
9C G 4.2 4.6 + - - +
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Residues in contact with THR 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A LEU* 3.4 7.1 - - - -
623A ARG* 1.3 67.3 - - - +
625A LEU* 1.3 58.2 + - - +
627A PHE* 3.2 10.1 + - + +
628A LEU* 2.9 42.3 + - + +
668A PHE* 3.1 42.1 - - + +
824A LEU* 4.1 16.4 - - + -
828A THR* 3.9 20.0 + - - +
7C G 4.3 0.9 + - - -
8C T 2.3 23.8 + - - -
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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
----------------------------------------------------------
419A SER* 4.4 15.1 + - - -
420A VAL 4.4 1.8 - - - +
421A GLY* 3.7 28.3 - - - +
467A ASP* 3.8 21.8 - - + -
468A PHE 3.8 15.9 - - - +
469A SER* 4.0 10.8 - - - +
622A LEU* 3.5 17.0 + - + +
623A ARG 3.1 0.4 - - - -
624A THR* 1.3 78.9 - - - +
626A THR* 1.3 62.8 + - - +
628A LEU* 3.1 18.5 + - + +
629A ASP* 3.1 20.1 + - - +
824A LEU* 3.6 37.2 - - + -
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Residues in contact with THR 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A SER* 3.6 4.5 + - - +
470A ASP* 2.4 57.5 + - - +
471A ARG* 3.5 33.3 + - + +
622A LEU 3.6 0.8 + - - -
623A ARG* 2.9 16.9 + - - +
625A LEU* 1.3 76.8 - - - +
627A PHE* 1.3 60.7 + - - +
629A ASP* 3.5 17.9 + - - +
630A GLU* 3.5 15.4 + - - +
846A VAL* 4.0 6.3 - - + -
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Residues in contact with PHE 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 ARG 2.9 7.4 + - - +
624A THR* 3.4 14.4 - - + +
626A THR* 1.3 73.8 - - - +
628A LEU* 1.3 75.5 + - + +
629A ASP 3.1 2.4 + - - -
630A GLU* 3.4 2.8 + - - +
631A ALA* 3.1 24.1 + - + +
828A THR* 4.6 11.4 - - + -
839A PHE* 3.4 34.5 - + - -
842A ALA* 2.8 23.8 - - + -
843A LEU* 2.4 68.6 - - + -
846A VAL* 2.9 31.8 - - + +
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Residues in contact with LEU 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A THR* 2.9 36.5 + - + +
625A LEU* 3.1 11.8 + - + +
627A PHE* 1.3 83.2 - - + +
629A ASP* 1.3 63.4 + - - +
631A ALA* 4.0 2.5 - - - -
632A ARG* 3.2 6.2 + - - +
645A TYR* 2.7 59.9 + - + +
824A LEU* 3.9 12.8 - - + +
827A GLN* 3.7 24.5 - - + +
828A THR* 4.0 28.7 - - - +
831A VAL* 4.5 4.5 - - + -
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Residues in contact with ASP 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 3.0 31.4 + - - -
469A SER* 3.9 14.4 + - - -
471A ARG* 5.4 5.6 - - - +
472A GLU* 5.9 0.3 - - - +
625A LEU 3.1 11.9 + - - +
626A THR* 3.6 10.1 - - - +
627A PHE 3.1 0.4 - - - -
628A LEU* 1.3 76.1 - - - +
630A GLU* 1.3 63.0 + - + +
632A ARG* 3.1 32.8 + - - +
633A ARG* 2.9 27.7 + - - +
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Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 3.0 43.8 + - - +
626A THR 3.5 8.3 + - - +
627A PHE 3.4 6.3 + - - +
629A ASP* 1.3 73.4 - - - +
631A ALA* 1.3 60.2 + - - +
633A ARG* 2.7 42.9 + - - +
634A ILE* 2.8 38.0 + - + +
842A ALA* 4.1 14.8 - - + -
845A SER* 4.1 16.8 + - - +
846A VAL* 4.9 8.1 - - + -
879A ASP* 4.9 1.2 - - - +
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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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627A PHE* 3.1 24.6 + - + +
628A LEU* 4.1 2.0 - - - -
629A ASP 3.2 0.2 - - - -
630A GLU* 1.3 77.9 - - - +
632A ARG* 1.3 58.0 + - - +
634A ILE* 3.7 2.8 - - - +
635A VAL* 2.8 37.3 + - - +
643A LEU* 4.9 0.7 - - + -
645A TYR* 3.6 15.0 - - - +
831A VAL* 4.3 22.9 - - + -
838A GLU* 5.2 1.7 - - - +
839A PHE* 4.9 2.5 - - + +
842A ALA* 3.8 15.1 - - + +
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Residues in contact with ARG 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 4.5 4.8 + - - -
628A LEU 3.2 7.6 + - - +
629A ASP* 3.1 39.1 + - - +
631A ALA* 1.3 77.7 - - - +
633A ARG* 1.3 62.4 + - - +
635A VAL* 3.8 1.9 - - - +
636A LYS* 3.1 24.3 + - - +
641A VAL 4.7 0.3 - - - +
642A GLU* 4.2 13.9 - - - +
643A LEU* 3.4 46.1 + - + +
645A TYR* 3.7 26.8 + - - +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A ASP 2.9 13.4 + - - +
630A GLU* 2.7 51.0 + - - +
631A ALA 3.3 0.2 - - - -
632A ARG* 1.3 80.2 - - - +
634A ILE* 1.3 98.4 + - - +
636A LYS* 3.3 6.2 + - - +
637A GLU* 3.2 32.1 + - + +
845A SER* 6.4 0.2 - - - -
880A PHE 5.8 1.8 + - - -
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Residues in contact with ILE 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 GLU* 2.8 23.2 + - + +
631A ALA 3.9 1.3 - - - +
633A ARG* 1.3 102.3 - - - +
635A VAL* 1.3 55.2 + - - +
637A GLU* 3.3 11.1 + - - +
638A SER* 2.8 32.8 + - - -
838A GLU* 2.4 58.3 - - + +
841A ALA* 4.7 8.7 - - + +
842A ALA* 4.3 15.5 - - + +
845A SER* 5.9 2.0 - - - -
880A PHE 5.1 6.3 - - - +
882A VAL* 5.6 4.7 - - + -
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ALA* 2.8 21.1 + - - +
632A ARG 3.8 3.6 - - - +
634A ILE* 1.3 75.6 - - - +
636A LYS* 1.3 63.5 + - - +
638A SER* 3.1 1.4 + - - -
639A LYS* 2.9 25.8 + - + +
640A GLY 3.7 2.3 + - - -
641A VAL* 3.4 32.8 - - + +
643A LEU* 3.8 29.8 - - + -
831A VAL* 5.3 4.0 - - + -
835A TYR* 4.0 31.4 - - + -
838A GLU* 4.2 16.4 - - + -
839A PHE 5.4 0.9 - - - +
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Residues in contact with LYS 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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632A ARG* 3.1 18.6 + - + +
633A ARG* 3.5 6.7 - - - +
635A VAL* 1.3 75.8 - - - +
637A GLU* 1.3 59.8 + - - +
640A GLY* 2.7 34.4 + - - +
641A VAL 3.4 19.5 - - - +
642A GLU* 3.4 34.3 - - + +
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Residues in contact with GLU 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 ARG* 3.2 27.5 + - + +
634A ILE* 3.9 9.9 - - - +
636A LYS* 1.3 80.3 - - - +
638A SER* 1.3 63.1 + - - +
640A GLY 4.9 0.3 + - - -
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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
----------------------------------------------------------
634A ILE* 2.8 16.2 + - - -
635A VAL 3.7 3.1 - - - -
637A GLU* 1.3 79.6 - - - +
639A LYS* 1.3 74.5 + - - +
640A GLY 3.9 0.2 - - - -
838A GLU* 2.1 39.1 + - - -
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Residues in contact with LYS 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A VAL* 2.9 11.9 + - - +
638A SER* 1.3 97.2 + - - +
640A GLY* 1.3 58.7 + - - +
641A VAL* 3.1 28.1 + - + +
835A TYR* 3.7 27.3 - - + -
836A PRO* 4.6 11.5 - - - +
838A GLU* 4.1 14.2 + - - -
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Residues in contact with GLY 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LYS* 2.7 33.1 + - - +
637A GLU 4.9 0.2 + - - -
638A SER 3.9 0.4 - - - -
639A LYS* 1.3 70.9 - - - +
641A VAL* 1.3 61.3 + - - +
642A GLU* 3.6 5.2 + - - +
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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
------------------------------------------------------------
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