Contacts of the strand formed by residues 30 - 39 (chain C) in PDB entry 5IXM
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 PHE 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.3 17.8 + - + -
27C ALA* 2.8 49.6 + - + +
28C PRO 3.5 0.4 - - - -
29C ASN* 1.3 91.4 - - + +
31C ASP* 1.3 72.8 + - - +
50C PHE* 3.5 28.0 - + + -
51C ARG 3.6 2.9 - - - -
52C TYR* 3.9 17.0 - - + -
54C LEU* 3.6 27.6 - - + -
604C C8E 3.7 37.9 - - + -
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Residues in contact with ASP 31 (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 TYR* 2.8 33.1 + - + +
25C ASN* 3.7 9.5 - - - +
26C ILE* 3.8 6.7 - - - +
27C ALA 4.2 2.4 - - - +
28C PRO 6.1 0.4 - - - -
30C PHE* 1.3 82.2 - - - +
32C ALA* 1.3 61.4 + - - +
49C GLU 4.3 0.2 - - - -
50C PHE* 3.1 11.4 - - - -
51C ARG* 2.8 71.9 + - + +
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Residues in contact with ALA 32 (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 TYR* 3.6 5.2 - - - -
24C TRP* 3.1 43.6 + - + -
25C ASN 4.3 2.8 - - - +
26C ILE* 3.5 21.1 - - + +
31C ASP* 1.3 77.3 - - - +
33C THR* 1.3 68.2 + - - +
34C ILE* 4.5 5.2 - - + -
49C GLU 3.1 10.5 - - - +
50C PHE* 4.7 7.9 - - + -
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Residues in contact with THR 33 (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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4C LEU* 5.4 6.8 - - + +
21C PRO* 4.7 7.4 - - + -
22C TYR 3.3 13.0 + - - +
23C TYR* 3.9 14.0 - - - +
32C ALA* 1.3 78.6 + - - +
34C ILE* 1.3 65.7 + - - +
35C THR* 3.5 18.6 - - - +
47C GLN 3.3 2.9 - - - +
48C ASN* 3.2 5.7 - - - -
49C GLU* 2.9 46.1 + - + +
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Residues in contact with ILE 34 (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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22C TYR* 2.9 50.3 + - + +
24C TRP* 4.1 33.4 - - + -
32C ALA* 4.5 3.1 - - + -
33C THR* 1.3 82.4 - - - +
35C THR* 1.3 64.2 + - - +
36C PRO* 3.8 3.6 - - + +
46C TRP* 3.9 28.3 - - + -
47C GLN 3.5 2.2 - - - -
48C ASN* 3.3 26.9 - - + +
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Residues in contact with THR 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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19C LEU* 3.5 31.9 - - + -
20C LEU 3.8 1.3 - - - +
21C PRO* 3.5 26.8 - - + +
33C THR* 3.5 18.7 - - - +
34C ILE* 1.3 80.7 + - - +
36C PRO* 1.3 68.1 - - - +
37C HIS 3.5 2.1 + - - -
46C TRP* 3.6 3.5 - - - -
47C GLN* 2.9 49.1 + - - +
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Residues in contact with PRO 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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3C PHE* 6.4 0.4 - - + -
18C PHE* 3.5 2.9 - - - +
19C LEU* 3.6 0.3 - - - -
20C LEU* 3.0 60.1 + - + +
22C TYR* 5.8 1.8 - - + -
34C ILE* 3.8 4.7 - - + +
35C THR* 1.3 88.0 - - - +
37C HIS* 1.3 60.1 + - - +
38C TYR 4.0 1.1 - - - -
44C LEU* 4.2 14.1 - - + -
45C GLN 3.5 7.4 - - - +
46C TRP* 3.5 34.1 - - + -
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Residues in contact with HIS 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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9C LYS* 5.7 2.2 - - + -
17C GLU* 3.2 30.6 + - + +
18C PHE 3.3 4.7 - - - -
19C LEU* 3.1 32.4 - - + +
35C THR 4.3 4.0 - - - +
36C PRO* 1.3 72.5 - - - +
38C TYR* 1.3 62.8 + - - +
39C MET* 3.3 35.7 + - + +
43C GLY 3.7 0.7 - - - +
44C LEU* 3.9 1.9 - - - +
45C GLN* 2.9 50.3 + - + +
47C GLN* 3.9 16.2 + - - +
118C THR* 5.3 13.2 - - + -
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Residues in contact with TYR 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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16C PHE* 4.4 7.6 - - + -
17C GLU* 3.2 6.1 - - - -
18C PHE* 2.9 55.0 + - + +
36C PRO 4.0 0.4 - - - -
37C HIS* 1.3 74.3 - - - +
39C MET* 1.3 71.6 + - - +
40C GLU* 3.6 38.9 + - + +
43C GLY* 3.8 12.3 - - - -
44C LEU* 4.0 15.8 - - + +
70C ARG* 5.2 3.7 + - - -
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Residues in contact with MET 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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14C ASN* 3.8 22.9 - - + -
16C PHE 3.7 3.4 - - - -
17C GLU* 3.8 12.3 - - + +
37C HIS* 3.3 30.7 - - + +
38C TYR* 1.3 76.8 - - - +
40C GLU* 1.3 67.7 + - - +
41C ARG 3.3 1.3 - - - -
42C ARG* 3.1 15.0 + - + +
43C GLY* 2.9 42.7 + - - +
45C GLN* 3.8 29.8 - - + +
66C LEU* 4.0 13.9 - - + -
117C LEU* 3.7 31.0 - - + -
118C THR 6.2 0.2 - - - -
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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