Contacts of the helix formed by residues 628 - 636 (chain A) in PDB entry 5N4D
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 ILE 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLN 4.7 0.2 - - - -
625A ASN* 3.0 37.2 + - + +
626A PRO 4.4 1.1 - - - -
627A SER* 1.3 81.2 - - - +
629A PRO* 1.3 69.2 - - + +
630A GLU* 3.5 20.9 - - + +
631A GLU* 2.9 34.0 + - + +
632A PHE* 2.9 21.0 + - - +
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Residues in contact with PRO 629 (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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24A GLN* 3.2 36.6 - - + +
25A SER 3.9 2.0 - - - -
26A ALA* 3.2 36.4 + - + +
627A SER 3.8 7.9 - - - +
628A ILE* 1.3 89.3 - - + +
630A GLU* 1.3 71.4 + - - +
632A PHE* 3.6 2.4 + - + +
633A ASP* 3.3 16.8 + - - +
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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
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26A ALA* 3.7 23.0 - - + +
628A ILE* 3.2 17.1 + - + +
629A PRO* 1.3 85.4 - - - +
631A GLU* 1.3 65.8 + - + +
633A ASP* 3.5 15.2 + - - +
634A TYR* 3.7 12.7 - - - -
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Residues in contact with GLU 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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543A ARG* 5.5 3.1 + - - -
620A ILE* 5.2 1.0 - - - +
624A GLY* 3.7 3.6 - - - -
625A ASN* 2.8 50.8 + - - +
628A ILE* 2.9 31.0 + - + +
630A GLU* 1.3 80.0 - - + +
632A PHE* 1.3 67.2 + - - +
633A ASP 3.1 0.9 - - - -
634A TYR* 3.0 35.5 + - + +
635A ILE* 3.0 27.8 + - + +
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Residues in contact with PHE 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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23A TYR* 3.4 37.9 - + + -
24A GLN 4.0 9.0 - - - +
25A SER* 4.1 9.4 - - - -
31A VAL* 4.3 24.0 - - + -
33A VAL* 4.6 0.2 - - + -
608A LEU* 3.5 26.7 - - + -
625A ASN 4.1 2.2 + - - -
626A PRO* 3.5 25.1 - - - +
628A ILE 2.9 11.3 + - - +
629A PRO 3.7 5.2 - - - +
631A GLU* 1.3 75.5 - - - +
633A ASP* 1.3 69.0 + - - +
635A ILE* 4.3 8.5 - - - -
636A TYR* 2.9 68.5 + + + +
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Residues in contact with ASP 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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25A SER* 2.4 33.4 + - - -
26A ALA* 3.2 11.8 + - - +
27A SER* 2.9 33.9 + - - +
629A PRO 3.3 8.1 + - - -
630A GLU 3.6 9.6 - - - +
631A GLU 3.1 1.6 - - - -
632A PHE* 1.3 80.7 - - - +
634A TYR* 1.3 57.1 + - + +
636A TYR* 5.3 0.7 - - - -
637A PRO* 3.3 20.6 - - - +
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Residues in contact with TYR 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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543A ARG* 3.5 35.5 + - - +
544A GLU* 3.7 38.3 + - + +
623A TYR 3.5 20.9 - - - -
624A GLY* 3.7 5.2 - - - -
630A GLU 3.7 15.0 - - - -
631A GLU* 3.0 47.2 + - + +
633A ASP* 1.3 77.3 - - - +
635A ILE* 1.3 69.4 + - + +
637A PRO* 3.6 9.9 - - - +
638A LEU* 4.0 18.5 - - - +
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Residues in contact with ILE 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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607A LEU* 3.2 43.5 - - + +
608A LEU* 4.2 7.2 - - + -
610A PHE* 5.2 1.1 - - + -
623A TYR* 3.3 18.6 - - + +
624A GLY* 3.5 33.4 - - - +
625A ASN 3.7 3.4 - - - +
626A PRO* 3.6 22.9 - - + -
631A GLU 3.0 21.9 + - - +
632A PHE* 3.2 4.2 + - - +
634A TYR* 1.3 84.1 - - + +
636A TYR* 1.3 67.0 + - - +
638A LEU* 2.9 16.7 + - - +
639A SER* 3.1 10.6 + - - -
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Residues in contact with TYR 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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31A VAL* 4.2 18.7 - - + +
32A PRO 4.9 2.3 + - - -
33A VAL* 3.9 23.9 - - + +
34A PRO* 5.9 0.5 - - - +
608A LEU* 3.6 37.4 - - + +
632A PHE* 2.9 39.3 + + + +
633A ASP* 5.3 0.4 - - - -
635A ILE* 1.3 78.5 - - - +
637A PRO* 1.3 62.0 - - + +
638A LEU 3.1 0.7 + - - -
639A SER* 3.3 4.9 + - - -
642A HIS* 3.9 22.3 + + + +
643A ASN* 2.9 20.8 + - - +
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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