Contacts of the helix formed by residues 25 - 32 (chain A) in PDB entry 1XZQ
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 ASP 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ASP* 6.0 0.3 - - - -
3A THR* 3.1 17.5 + - - -
24A PRO* 1.3 82.4 - - - +
26A SER* 1.3 63.8 + - - +
27A TRP 3.1 3.5 + - - -
28A LYS* 3.3 34.2 + - + +
29A ILE* 2.8 41.3 + - + +
99A GLY* 5.0 7.4 - - - +
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Residues in contact with SER 26 (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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3A THR* 3.5 14.2 + - - -
21A LEU* 3.6 12.6 - - - +
23A GLY 3.1 27.0 + - - -
24A PRO 3.0 1.2 + - - -
25A ASP* 1.3 77.0 - - - +
27A TRP* 1.3 69.9 + - - +
29A ILE* 4.0 1.1 - - - +
30A VAL* 3.4 12.1 + - - +
75A ASP* 3.1 27.8 + - - +
77A VAL* 3.3 29.5 - - - +
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Residues in contact with TRP 27 (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 PRO 4.3 3.1 + - - +
25A ASP 3.1 0.4 - - - -
26A SER* 1.3 93.8 + - - +
28A LYS* 1.3 72.4 + - + +
29A ILE 3.2 0.3 + - - -
30A VAL* 3.3 8.5 + - - +
31A GLN* 2.9 45.0 + - - +
40A ILE* 4.0 31.9 - - + -
42A PRO* 4.8 11.9 - - + -
64A PHE* 3.7 38.4 - + + -
65A TYR 3.3 28.8 + - - -
66A LYS* 3.2 41.1 - - + -
75A ASP* 3.7 13.9 + - + -
76A MET 3.8 9.1 + - - -
77A VAL* 4.9 0.2 - - + -
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Residues in contact with LYS 28 (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 PRO* 3.9 10.1 + - - +
25A ASP* 3.3 45.0 + - + +
27A TRP* 1.3 77.7 - - + +
29A ILE* 1.3 59.0 + - + +
31A GLN* 3.7 6.4 + - - -
32A LYS* 2.8 35.9 + - - +
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Residues in contact with ILE 29 (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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3A THR* 3.5 29.6 - - + -
21A LEU* 4.5 4.0 - - + -
25A ASP* 2.8 41.5 + - + +
26A SER* 4.0 3.8 - - - +
28A LYS* 1.3 76.6 - - + +
30A VAL* 1.3 61.3 + - - +
32A LYS* 4.7 1.6 - - - -
33A HIS* 3.2 25.3 + - - -
95A PHE* 3.7 30.0 - - + +
98A SER* 3.8 38.1 - - - +
99A GLY* 4.2 0.9 - - - -
100A ALA* 3.9 13.0 - - + +
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Residues in contact with VAL 30 (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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21A LEU* 3.8 6.5 - - + +
26A SER 3.4 9.1 + - - +
27A TRP 3.3 9.6 + - - +
29A ILE* 1.3 79.2 - - - +
31A GLN* 1.3 60.8 + - - +
32A LYS 3.3 0.4 + - - -
33A HIS* 3.6 4.2 + - - +
34A LEU* 3.0 27.6 + - + +
50A ILE* 4.6 8.2 - - + +
62A VAL* 4.6 7.9 - - + -
64A PHE* 3.7 9.9 - - + -
77A VAL* 3.4 27.8 - - + -
79A VAL* 3.4 29.2 - - + -
95A PHE* 3.6 22.7 - - + -
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Residues in contact with GLN 31 (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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27A TRP* 2.9 40.5 + - - +
28A LYS* 3.8 5.8 + - - +
30A VAL* 1.3 76.4 - - + +
32A LYS* 1.3 64.7 + - - +
33A HIS 3.1 2.5 - - - -
34A LEU* 3.2 29.0 + - + +
40A ILE* 3.0 52.6 - - + +
64A PHE* 4.8 4.9 - - + -
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Residues in contact with LYS 32 (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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28A LYS 2.8 17.8 + - - +
29A ILE* 3.5 2.5 - - - +
30A VAL 3.3 0.2 - - - -
31A GLN* 1.3 77.4 - - - +
33A HIS* 1.3 86.6 + - + +
34A LEU 5.1 0.4 - - - +
51A HIS* 4.0 8.7 - - - -
98A SER* 3.5 20.5 + - - +
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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