Contacts of the strand formed by residues 34 - 40 (chain C) in PDB entry 1AXC
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 GLY 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ASP 3.6 2.4 - - - +
30C ILE* 3.7 0.2 - - - -
31C SER* 2.8 29.7 + - - -
32C SER 3.3 0.2 - - - -
33C SER* 1.3 81.7 + - - +
35C VAL* 1.3 61.8 + - - -
36C ASN* 3.9 5.2 + - - -
52C LEU 3.3 10.5 - - - -
53C ARG* 4.5 0.2 - - - -
54C SER* 3.6 6.3 - - - -
60C TYR* 3.3 20.6 + - - -
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C PHE* 4.6 11.7 - - + -
28C TRP* 3.5 39.3 - - + -
29C ASP 3.7 4.5 - - - +
30C ILE* 4.3 17.7 - - + +
34C GLY* 1.3 73.9 - - - -
36C ASN* 1.3 69.7 + - - +
50C LEU* 3.8 4.3 - - + +
51C THR* 3.5 4.3 + - - +
52C LEU* 2.9 49.6 + - + +
57C PHE* 4.4 19.1 - - + -
60C TYR* 4.4 6.3 - - + +
90C LEU* 5.4 6.3 - - + -
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TRP* 3.8 1.4 - - - -
29C ASP* 2.8 52.2 + - + +
31C SER* 5.2 3.4 - - - -
33C SER* 3.9 19.2 + - - -
34C GLY* 4.1 6.9 + - - -
35C VAL* 1.3 79.1 - - - +
37C LEU* 1.3 62.1 + - - +
49C GLN* 4.1 5.1 + - - +
50C LEU 3.3 2.4 - - - +
51C THR* 3.0 33.1 + - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.3 12.1 - - + -
23C ILE* 4.3 11.2 - - + -
26C ALA* 3.9 13.0 - - + -
27C CYS 3.8 13.0 - - - +
28C TRP* 3.4 49.6 - - + +
29C ASP* 5.0 1.1 - - - -
36C ASN* 1.3 76.6 - - - +
38C GLN* 1.3 68.6 + - - +
39C SER* 4.3 1.6 - - - +
48C VAL* 4.2 21.3 - - + -
49C GLN* 3.2 6.0 + - - +
50C LEU* 2.7 53.9 + - + +
72C LEU* 4.5 3.8 - - + -
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Residues in contact with GLN 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C CYS 4.5 6.6 + - - +
29C ASP* 5.2 2.0 + - - +
37C LEU* 1.3 75.0 - - - +
39C SER* 1.3 65.8 + - - +
47C LEU* 4.0 19.4 - - + +
48C VAL 3.1 13.5 - - - +
49C GLN* 4.3 16.6 - - + +
123C VAL* 4.6 4.5 - - - +
124C GLU 4.8 0.9 - - - +
125C GLN* 3.4 45.0 + - - +
126C LEU 2.9 47.2 + - - -
128C ILE* 4.3 14.1 - - - +
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Residues in contact with SER 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.9 25.7 - - - +
25C GLU 3.7 15.2 + - - -
26C ALA* 4.0 16.3 - - - +
27C CYS 5.5 0.2 - - - -
37C LEU* 4.3 1.3 - - - +
38C GLN* 1.3 77.8 - - - +
40C MET* 1.3 74.5 + - - +
41C ASP 4.3 0.2 + - - -
47C LEU* 3.3 7.0 - - - +
48C VAL* 2.7 36.8 + - - +
123C VAL* 5.6 6.8 - - - +
124C GLU 5.7 2.9 - - - -
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Residues in contact with MET 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 4.0 3.3 - - - +
39C SER* 1.3 84.2 + - - +
41C ASP* 1.3 64.7 + - - +
42C SER 3.9 0.2 + - - -
44C HIS* 3.3 57.8 + - + +
46C SER 3.5 17.3 - - - +
47C LEU* 3.9 20.9 - - + +
124C GLU* 4.1 26.1 + - + +
126C LEU* 4.2 6.3 - - + -
147D MET* 4.1 12.1 - - + -
148D THR* 3.4 26.5 - - + -
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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