Contacts of the strand formed by residues 46 - 53 (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 SER 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C LEU* 3.7 23.1 - - - +
40C MET* 3.5 10.0 - - - +
41C ASP* 2.9 41.3 + - - +
45C VAL* 1.3 78.6 - - - +
47C LEU* 1.3 62.3 + - - +
211C TYR* 4.0 12.3 - - - -
215C PHE* 3.8 19.5 - - - -
250C TYR 2.9 14.6 - - - -
251C LEU* 4.5 1.3 - - - -
147D MET* 3.9 3.6 - - - -
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Residues in contact with LEU 47 (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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38C GLN* 4.0 23.6 - - + +
39C SER 3.3 13.5 - - - +
40C MET* 3.9 17.7 - - + +
41C ASP 5.0 0.4 - - - +
46C SER* 1.3 77.3 - - - +
48C VAL* 1.3 68.6 + - - +
49C GLN* 4.9 0.2 - - + -
124C GLU 6.0 0.9 - - - +
126C LEU* 3.4 39.5 - - + -
128C ILE* 3.5 27.1 - - + -
215C PHE* 5.4 0.2 - - - -
249C TYR* 3.4 4.9 - - - +
250C TYR* 2.7 50.7 + - + -
147D MET* 3.9 13.0 - - + -
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.3 33.4 - - + -
22C LEU* 3.6 32.1 - - + -
23C ILE* 3.8 18.4 - - + -
37C LEU* 4.2 12.3 - - + -
38C GLN* 3.1 9.9 - - - +
39C SER 2.7 33.1 + - - +
47C LEU* 1.3 77.1 - - - +
49C GLN* 1.3 66.2 + - - +
50C LEU 4.4 0.2 - - - +
247C LEU* 3.5 17.5 - - + -
248C LYS 3.4 4.0 - - - +
249C TYR* 3.9 7.4 - - + -
250C TYR* 5.2 0.2 - - - -
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Residues in contact with GLN 49 (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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36C ASN* 4.1 6.1 + - - +
37C LEU 3.2 11.0 + - - +
38C GLN* 4.3 19.7 - - + +
48C VAL* 1.3 78.4 - - - +
50C LEU* 1.3 76.8 + - - +
51C THR* 2.9 21.0 + - - -
128C ILE* 6.3 0.4 - - + -
246C HIS* 2.8 29.1 + - - -
247C LEU* 3.6 1.2 - - - -
248C LYS* 2.8 45.3 + - + +
250C TYR* 4.2 20.6 - - + +
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Residues in contact with LEU 50 (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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15C VAL* 3.7 35.2 - - + -
19C LEU* 4.5 2.7 - - + -
28C TRP* 4.2 22.4 - - + -
35C VAL* 4.9 3.8 - - + +
36C ASN* 3.3 3.6 - - - -
37C LEU* 2.7 61.6 + - + +
48C VAL 4.2 0.2 - - - -
49C GLN* 1.3 78.8 + - - +
51C THR* 1.3 68.3 + - - +
52C LEU* 4.3 14.4 - - + -
241C ILE* 3.9 16.8 - - + -
246C HIS 3.8 10.8 - - - +
247C LEU* 4.0 16.2 - - + -
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Residues in contact with THR 51 (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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35C VAL 3.5 3.8 - - - +
36C ASN* 3.0 17.1 + - - +
49C GLN* 2.9 28.8 + - - -
50C LEU* 1.3 71.7 - - - +
52C LEU* 1.3 68.9 + - - +
53C ARG* 3.9 21.8 - - + +
245C GLY* 3.3 4.9 - - - -
246C HIS* 3.1 58.8 + - + +
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Residues in contact with LEU 52 (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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11C ILE* 4.7 2.7 - - + -
12C LEU* 4.1 25.8 - - + -
15C VAL* 4.7 5.2 - - + -
28C TRP* 5.1 1.6 - - + -
34C GLY* 3.3 1.3 - - - -
35C VAL* 2.9 52.2 + - + +
50C LEU* 4.3 17.9 - - + -
51C THR* 1.3 77.2 - - - +
53C ARG* 1.3 66.4 + - - +
57C PHE* 3.9 14.6 - - + -
90C LEU* 6.5 0.2 - - + -
241C ILE* 3.7 30.3 - - + -
244C MET* 3.7 38.6 - - + -
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Residues in contact with ARG 53 (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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33C SER 3.6 8.5 - - - +
51C THR* 4.4 15.1 - - + +
52C LEU* 1.3 74.1 - - - +
54C SER* 1.3 56.9 + - - +
55C GLU* 3.4 21.3 - - + +
56C GLY* 2.7 30.3 + - - +
57C PHE* 3.5 6.1 - - - -
240C LYS* 6.2 1.0 - - - +
243C ASP* 4.4 18.0 + - - +
244C MET* 2.7 21.8 + - - +
245C GLY* 3.6 31.0 + - - +
246C HIS* 5.5 2.4 + - - -
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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