Contacts of the strand formed by residues 29 - 36 (chain C) in PDB entry 5FQD
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 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C SER* 3.3 2.6 - - - -
26C GLY* 2.8 35.3 + - - +
27C SER 3.6 2.0 - - - -
28C PHE* 1.3 85.4 - - - +
30C ASP* 1.4 64.8 + - - +
47C LEU 3.4 9.9 - - - -
48C GLU* 4.7 0.7 - - - -
49C SER 5.5 0.2 - - - -
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Residues in contact with ASP 30 (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 LYS* 3.5 35.5 + - + +
24C GLY 3.5 9.2 - - - +
25C SER* 3.1 20.5 + - - +
28C PHE* 3.7 1.6 - - - -
29C GLY* 1.4 76.2 - - - -
31C ILE* 1.3 63.8 + - - +
32C TYR* 3.8 23.1 + - + -
45C VAL 3.8 0.7 - - - +
46C LYS* 3.5 3.1 - - - -
47C LEU* 2.9 37.6 + - + +
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Residues in contact with ILE 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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22C LYS* 3.6 3.5 - - - +
23C ILE* 2.7 48.5 + - + -
24C GLY* 3.1 20.2 + - - +
25C SER 3.7 23.1 - - - +
28C PHE* 3.9 17.5 - - + -
30C ASP* 1.3 78.0 - - - +
32C TYR* 1.3 57.6 + - - +
44C ALA* 4.3 15.0 - - + -
45C VAL 3.4 8.3 - - - +
46C LYS* 3.9 21.1 - - + +
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Residues in contact with TYR 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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19C LEU* 4.0 32.5 - - + -
20C VAL 5.4 0.2 - - - -
21C ARG* 3.3 10.3 - - - +
22C LYS* 3.5 49.5 - - + -
23C ILE* 3.7 7.4 - - - +
30C ASP* 3.8 24.7 + - + -
31C ILE* 1.3 76.0 - - - +
33C LEU* 1.3 62.1 + - - +
44C ALA* 3.3 8.0 - - - +
45C VAL* 2.8 43.9 + - + +
47C LEU* 3.7 32.9 - - + +
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Residues in contact with LEU 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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19C LEU* 3.7 2.1 - - - -
20C VAL* 2.8 47.7 + - + +
21C ARG* 2.7 53.5 + - + +
23C ILE* 3.8 19.3 - - + +
32C TYR* 1.3 72.5 - - - +
34C ALA* 1.3 58.1 + - - +
42C GLU* 3.9 28.9 - - + +
43C VAL 3.6 6.7 - - - +
92C LEU* 3.7 32.5 - - + -
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Residues in contact with ALA 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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17C TYR* 4.2 5.4 - - + -
18C LYS 3.2 13.9 - - - +
19C LEU* 4.0 10.5 - - + -
20C VAL* 4.3 2.7 - - - +
33C LEU* 1.3 75.6 - - - +
35C ILE* 1.3 61.6 + - - +
42C GLU* 3.4 7.3 - - - +
43C VAL* 2.9 40.5 + - + -
45C VAL* 3.5 31.9 - - + -
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Residues in contact with ILE 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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353B HIS* 5.2 4.9 - - - +
377B GLU* 5.2 10.1 - - - +
386B TRP* 5.2 5.4 - - + -
17C TYR* 4.3 2.9 - - - -
18C LYS* 2.8 57.3 + - + +
20C VAL* 3.9 17.5 - - + -
34C ALA* 1.3 75.5 - - - +
36C ASN* 1.3 65.7 + - - +
37C ILE* 3.2 10.3 + - + +
40C GLY* 3.4 36.3 - - - +
41C GLU 3.3 2.7 - - - +
42C GLU* 4.4 15.5 - - + +
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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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16C LYS* 3.3 39.4 - - - +
17C TYR* 3.9 15.3 + - + -
34C ALA 4.4 0.2 - - - -
35C ILE* 1.3 68.3 - - - +
37C ILE* 1.3 57.2 + - - +
38C THR* 2.7 44.1 + - - +
39C ASN* 3.5 27.2 - - - +
40C GLY* 2.9 31.2 + - - -
41C GLU* 2.7 36.8 + - - +
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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