Contacts of the helix formed by residues 629 - 643 (chain A) in PDB entry 5I35
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 CYS 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A LEU* 4.2 7.9 - - - -
569A ALA* 3.4 30.1 + - + +
570A PHE* 3.5 23.0 - - + -
572A SER 4.4 1.4 + - - -
574A GLU 4.8 0.6 + - - -
576A PHE* 4.5 3.3 - - - +
578A PHE* 3.6 31.4 - - - -
627A PHE* 3.6 22.4 - - - -
628A PRO* 1.3 72.4 - - - +
630A LYS* 1.3 66.6 + - - +
631A ALA 3.4 2.0 - - - -
632A MSE 3.0 24.8 - - + +
633A PHE 3.2 5.4 + - - -
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Residues in contact with LYS 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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569A ALA 3.8 1.2 + - - -
570A PHE 3.4 20.4 - - - +
571A ALA* 3.9 20.0 - - - +
572A SER 3.3 20.9 + - - +
573A ASP* 4.1 22.0 - - + +
628A PRO* 3.7 1.8 - - - +
629A CYS* 1.3 78.7 - - - +
631A ALA* 1.3 59.7 + - - +
633A PHE* 3.2 3.3 + - - +
634A GLU* 2.9 50.5 + - + +
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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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469A TYR* 5.6 3.8 - - - +
573A ASP* 5.1 5.6 + - - +
628A PRO* 5.4 2.9 + - + +
629A CYS 3.4 0.4 - - - -
630A LYS* 1.3 77.6 - - - +
632A MSE 1.3 66.8 + - - +
634A GLU* 4.1 4.8 - - - +
635A GLU* 3.0 26.9 + - - +
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Residues in contact with MSE 632 (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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469A TYR* 3.4 55.1 + - + +
472A LEU* 3.8 30.5 - - - -
473A VAL* 3.7 28.9 - - + -
476A LEU* 4.0 17.1 - - + +
570A PHE* 4.5 2.0 - - + -
627A PHE* 3.7 17.7 - - + -
628A PRO 4.2 3.3 + - - +
629A CYS* 3.0 28.4 - - + +
631A ALA* 1.3 79.0 - - - +
633A PHE* 1.3 55.9 + - - +
635A GLU* 3.4 6.1 + - - +
636A ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 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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476A LEU* 4.2 17.5 - - + -
480A PHE* 4.7 5.4 - + - -
523A ILE* 4.4 16.8 - - + -
526A ILE* 3.7 22.0 - - + -
527A ARG* 3.7 61.5 - - - -
530A ALA* 4.1 8.1 - - + -
570A PHE* 3.4 42.0 - + + +
629A CYS 3.2 8.5 + - - +
630A LYS 3.8 2.5 - - - +
632A MSE 1.3 79.0 - - - +
634A GLU* 1.3 59.6 + - - +
636A ALA* 3.1 4.1 + - + +
637A TYR* 2.8 44.2 + + + +
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Residues in contact with GLU 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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527A ARG* 2.6 45.5 + - - -
570A PHE 5.0 1.9 - - - +
630A LYS* 2.9 48.6 + - + +
631A ALA* 4.1 4.7 - - - +
633A PHE* 1.3 74.5 - - + +
635A GLU* 1.3 52.4 + - - +
637A TYR* 3.4 5.7 + - - +
638A SER* 2.8 38.0 + - - -
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Residues in contact with GLU 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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631A ALA 3.0 17.7 + - - +
632A MSE 3.5 6.1 - - - +
634A GLU* 1.3 75.3 - - - +
636A ALA* 1.3 63.8 + - - +
638A SER* 3.2 6.3 + - - -
639A ASN* 3.0 47.1 + - - +
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Residues in contact with ALA 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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476A LEU* 4.2 28.9 - - + +
480A PHE* 4.7 16.4 - - + +
523A ILE* 5.3 2.0 - - - -
632A MSE 2.9 20.0 + - - +
633A PHE* 3.8 5.2 - - + +
635A GLU* 1.3 75.6 - - - +
637A TYR* 1.3 63.5 + - - +
639A ASN* 3.4 4.6 + - - +
640A TYR* 3.0 25.5 + - - +
643A ARG* 5.2 0.5 + - - -
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Residues in contact with TYR 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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523A ILE* 3.8 33.2 - - + -
524A GLN* 5.7 2.7 - - + +
527A ARG* 3.4 59.9 - - + +
633A PHE* 2.8 32.3 + + + +
634A GLU* 3.8 5.2 - - - +
636A ALA* 1.3 72.4 - - - +
638A SER* 1.3 67.1 + - - +
640A TYR* 3.5 5.7 + + - +
641A CYS* 3.2 45.2 + - - -
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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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634A GLU 2.8 19.8 + - - -
635A GLU* 3.2 5.8 + - - -
637A TYR* 1.3 81.0 - - - +
639A ASN* 1.3 64.2 + - - +
641A CYS* 3.2 7.7 + - - +
642A LYS* 2.9 44.4 + - - +
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Residues in contact with ASN 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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635A GLU* 3.0 42.7 + - - +
636A ALA* 4.3 4.1 - - - +
638A SER* 1.3 79.7 + - - +
640A TYR* 1.3 66.5 + - - +
642A LYS* 3.8 18.4 - - + +
643A ARG* 3.0 44.5 + - - +
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Residues in contact with TYR 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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480A PHE* 3.6 33.0 - + + +
516A ARG* 4.9 2.0 - - - -
519A THR* 5.2 4.7 - - - -
520A ASP* 2.0 47.6 + - - +
523A ILE* 3.7 34.3 - - + +
636A ALA 3.0 17.7 + - - +
637A TYR* 3.7 8.3 - + - +
639A ASN* 1.3 79.1 - - - +
641A CYS* 1.3 70.6 + - - +
643A ARG* 3.5 26.8 + - - +
644A GLN* 3.3 43.9 + - - +
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Residues in contact with CYS 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 TYR* 3.2 50.4 + - - +
638A SER* 3.2 9.6 + - - +
640A TYR* 1.3 80.9 - - - +
642A LYS* 1.3 65.5 + - - +
644A GLN* 3.3 23.9 - - - +
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Residues in contact with LYS 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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638A SER* 2.9 32.1 + - - +
639A ASN* 3.8 19.3 - - + +
640A TYR 3.4 0.2 - - - -
641A CYS* 1.3 74.8 - - - +
643A ARG* 1.3 58.3 + - - +
644A GLN 2.9 18.4 + - - +
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Residues in contact with ARG 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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480A PHE 2.8 28.1 + - - -
481A GLU* 3.8 33.8 + - - +
636A ALA 5.2 0.4 + - - -
639A ASN* 3.0 47.8 + - - +
640A TYR* 3.5 26.4 - - - +
641A CYS 3.4 0.6 - - - -
642A LYS* 1.3 74.4 - - - +
644A GLN* 1.3 66.1 + - - +
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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