Contacts of the strand formed by residues 20 - 26 (chain C) in PDB entry 3C5C
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 GLU 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY* 3.2 32.6 + - - +
18C PRO 4.2 4.9 - - - +
19C LEU* 1.3 79.3 - - - +
21C VAL* 1.3 64.6 + - - +
22C ASN* 4.3 7.2 - - - +
69C HIS* 3.3 27.9 + - + +
71C ARG* 5.6 7.1 - - + +
92C HIS* 3.9 15.8 + - + -
184C ARG* 5.5 0.2 + - - -
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Residues in contact with VAL 21 (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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20C GLU* 1.3 78.3 - - - +
22C ASN* 1.3 66.0 + - - +
23C LEU* 3.9 25.6 - - + -
68C VAL* 3.4 29.2 - - + -
69C HIS 3.0 6.1 + - - +
70C LEU* 3.6 10.1 - - + +
71C ARG 3.0 26.9 + - - +
92C HIS* 3.6 3.6 - - - +
180C VAL* 3.9 12.1 - - + -
183C ALA* 3.9 19.3 - - + -
184C ARG* 3.8 27.4 - - + +
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Residues in contact with ASN 22 (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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20C GLU* 5.2 5.5 + - - +
21C VAL* 1.3 71.8 + - - +
23C LEU* 1.3 63.0 + - - +
71C ARG* 3.4 27.2 - - - +
90C TRP* 3.1 62.7 + - + +
91C ALA 3.6 0.5 - - - -
92C HIS* 2.7 55.5 + - - +
93C ALA 3.2 6.9 + - - -
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Residues in contact with LEU 23 (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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21C VAL* 3.9 15.9 - - + -
22C ASN* 1.3 72.8 - - - +
24C ALA* 1.3 62.1 + - - +
25C ILE* 4.1 3.3 + - + -
70C LEU* 3.5 29.4 - - + -
71C ARG 2.9 11.8 + - - +
72C VAL* 3.3 10.3 - - + +
73C MET 2.8 26.5 + - - +
90C TRP* 3.7 4.6 - - - -
93C ALA* 3.5 24.5 - - + +
95C LEU* 5.5 5.2 - - + -
176C PHE* 4.0 30.1 - - + +
179C ALA* 3.6 36.8 - - + -
180C VAL* 4.4 0.7 - - + -
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Residues in contact with ALA 24 (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 LEU* 1.3 73.0 - - - +
25C ILE* 1.3 61.7 + - - +
26C LEU* 4.0 5.1 + - + -
73C MET* 3.6 9.0 - - + +
75C THR* 5.1 0.2 - - + -
87C TYR* 4.0 18.4 - - + -
90C TRP* 4.5 4.9 - - + -
91C ALA* 3.7 13.1 - - + +
93C ALA 3.1 7.3 + - - -
94C PHE* 3.2 30.9 - - + +
95C LEU 2.8 27.1 + - - +
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Residues in contact with ILE 25 (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 LEU* 5.0 2.0 - - + +
24C ALA* 1.3 74.1 - - - +
26C LEU* 1.3 56.4 + - - +
33C LYS* 3.7 23.5 - - + +
36C LEU* 5.5 2.0 - - + -
37C THR* 3.2 26.7 - - - +
72C VAL* 3.6 23.3 - - + -
73C MET 2.9 13.3 + - - +
74C ASP* 4.6 4.9 - - - -
75C THR* 2.7 35.7 + - - +
95C LEU* 3.3 19.5 - - + +
97C VAL* 3.6 28.7 - - + -
176C PHE* 3.7 22.0 - - + -
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Residues in contact with LEU 26 (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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24C ALA* 4.4 5.4 - - + +
25C ILE* 1.3 73.9 - - - +
27C GLY* 1.3 53.9 + - - +
33C LYS* 3.3 10.2 - - - +
75C THR* 3.6 32.1 - - + +
77C ASP* 4.9 1.3 - - - +
87C TYR* 3.7 39.3 - - + -
94C PHE* 3.8 27.8 - - + -
95C LEU 2.9 10.2 + - - +
96C VAL* 3.4 12.6 - - + -
97C VAL* 2.7 31.9 + - - +
112C TYR* 4.0 24.2 - - + -
115C LEU* 5.6 0.4 - - + -
116C LEU* 4.4 12.6 - - + -
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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