Contacts of the helix formed by residues 628 - 638 (chain A) in PDB entry 5XA0
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 PRO 628 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A LEU 3.7 1.1 - - - +
622A VAL* 3.3 38.7 - - + +
625A ASN* 3.4 4.9 - - - -
626A ARG 3.3 6.5 - - - +
627A GLU* 1.3 81.8 - - - +
629A ARG* 1.3 71.7 + - - +
630A PHE 3.3 1.8 - - - -
631A LEU* 3.4 7.0 + - + -
632A ASP* 2.7 22.7 + - + +
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Residues in contact with ARG 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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589A VAL* 2.9 35.9 - - + -
592A GLU* 5.3 2.5 - - + -
625A ASN* 3.7 13.4 - - + +
627A GLU* 3.2 7.5 + - + -
628A PRO* 1.3 80.6 - - - +
630A PHE* 1.3 57.6 + - - +
632A ASP* 2.7 22.8 + - - +
633A TYR* 3.1 13.1 + - - +
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Residues in contact with PHE 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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589A VAL* 4.9 1.1 - - + +
592A GLU* 5.3 7.4 - - - +
617A THR* 3.8 5.6 - - - +
618A PHE* 5.1 0.4 - - - -
621A LEU* 2.9 33.4 + - + +
625A ASN* 5.1 0.2 - - - +
628A PRO 3.3 0.6 - - - -
629A ARG* 1.3 78.9 - - - +
631A LEU* 1.3 62.0 + - - +
633A TYR* 3.5 6.3 + - - +
634A LEU* 3.1 20.0 + - - +
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Residues in contact with LEU 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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618A PHE* 3.5 37.9 - - + +
621A LEU* 4.2 3.2 - - - +
622A VAL* 4.4 8.3 - - + -
628A PRO* 3.4 9.3 + - + +
629A ARG 3.2 0.6 - - - -
630A PHE* 1.3 78.6 - - - +
632A ASP* 1.3 55.4 + - - +
634A LEU* 2.6 36.7 + - - +
635A SER* 2.8 7.8 + - - -
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Residues in contact with ASP 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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627A GLU 4.9 2.9 - - - +
628A PRO* 2.7 17.2 + - + +
629A ARG* 2.7 18.2 + - - +
631A LEU* 1.3 69.1 - - - +
633A TYR* 1.3 65.0 + - - +
635A SER* 2.9 17.9 + - - -
636A ASP* 3.0 10.7 + - - +
695A GLU* 6.0 6.7 - - + -
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Residues in contact with TYR 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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592A GLU* 4.4 30.5 - - + +
595A ILE* 5.5 4.7 - - + -
596A THR* 4.6 16.5 - - - +
629A ARG 3.1 6.9 + - - +
630A PHE 4.0 6.3 - - - +
632A ASP* 1.3 77.7 - - - +
634A LEU* 1.3 57.9 + - - +
636A ASP* 2.9 26.1 + - - +
637A LEU* 3.1 13.7 + - - +
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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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614A GLU* 6.4 2.0 - - + -
618A PHE* 5.0 7.6 - - + -
630A PHE 3.1 13.8 + - - +
631A LEU* 2.6 25.6 + - + +
633A TYR* 1.3 72.5 - - - +
635A SER* 1.3 60.0 + - - +
637A LEU* 3.5 14.9 + - - +
638A CYS* 3.9 3.5 + - - -
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Residues in contact with SER 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 LEU 2.8 12.4 + - - -
632A ASP* 2.9 9.4 + - - -
634A LEU* 1.3 70.9 - - - +
636A ASP* 1.3 69.9 + - - +
637A LEU 3.2 0.7 + - - -
638A CYS* 3.4 13.0 + - - +
699A PHE* 3.9 31.1 - - - -
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Residues in contact with ASP 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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596A THR* 6.1 4.5 - - - -
632A ASP 3.0 8.3 + - - +
633A TYR* 2.9 18.9 + - + +
635A SER* 1.3 76.1 - - - +
637A LEU* 1.3 67.4 + - - +
638A CYS* 3.2 5.2 + - - +
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Residues in contact with LEU 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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596A THR* 6.3 0.2 - - - -
599A LEU* 2.7 44.5 - - + +
600A HIS* 5.1 4.4 + - - +
633A TYR 3.1 6.8 + - - +
634A LEU* 3.8 11.7 - - - +
635A SER 3.2 0.4 - - - -
636A ASP* 1.3 80.8 - - - +
638A CYS* 1.3 72.6 + - - +
639A VAL* 3.1 7.1 + - + +
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Residues in contact with CYS 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 LEU 3.9 3.8 + - - -
635A SER 3.4 10.5 + - - +
636A ASP 3.2 9.0 + - - +
637A LEU* 1.3 80.0 - - - +
639A VAL* 1.3 73.0 + - - +
640A SER 4.8 0.4 - - - -
643A LYS* 2.9 25.7 - - - +
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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