Contacts of the strand formed by residues 25 - 30 (chain C) in PDB entry 5ANC
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 LYS 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.7 7.4 - - - +
24C ASP* 1.3 81.0 + - + +
26C MET* 1.3 60.8 + - - +
71C LYS* 4.5 4.9 - - - +
89C PHE* 3.6 6.6 - - - -
90C CYS* 2.8 45.9 + - + +
91C LYS* 5.4 1.8 - - - +
92C ASP 3.9 20.9 - - - +
93C ASN* 5.5 1.1 - - - +
94C ILE* 5.3 10.8 - - - +
97C VAL* 5.8 2.2 - - + -
192C TYR 4.4 6.5 - - - +
193C ASP* 3.4 50.0 + - - +
194C ALA* 4.7 6.3 - - - +
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Residues in contact with MET 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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21C THR* 3.5 24.7 - - - +
25C LYS* 1.3 78.0 - - - +
27C ILE* 1.3 63.2 + - - +
28C VAL* 3.5 32.1 - - + -
62C LYS* 5.1 6.7 - - - +
71C LYS* 5.1 12.3 - - + +
80C TYR* 4.9 10.1 - - + -
87C ILE* 3.7 26.9 - - + -
88C ILE 3.4 7.4 - - - +
89C PHE* 4.4 8.5 - - + -
90C CYS* 4.3 1.8 - - - +
192C TYR* 2.6 67.8 + - + +
194C ALA 5.8 0.2 - - - +
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Residues in contact with ILE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C MET* 1.3 80.4 - - - +
28C VAL* 1.3 62.7 + - - +
29C ALA* 3.5 4.2 + - + -
87C ILE* 3.6 1.3 - - - -
88C ILE* 2.8 58.5 + - + +
90C CYS* 3.7 15.9 - - - -
97C VAL* 3.5 41.5 - - + +
100C VAL* 4.0 9.4 - - + -
101C ILE* 4.4 18.2 - - + -
188C PRO* 5.7 2.0 - - + -
190C ILE 4.1 7.4 - - - +
191C ILE* 3.9 25.4 - - + -
192C TYR 4.0 8.1 - - - +
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Residues in contact with VAL 28 (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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26C MET* 3.5 30.7 - - + -
27C ILE* 1.3 69.4 - - - +
29C ALA* 1.3 51.7 + - - +
80C TYR* 3.5 32.8 - - + +
85C THR* 3.5 12.3 - - + +
86C CYS 3.5 15.7 - - - +
87C ILE* 4.3 9.0 - - + -
188C PRO* 4.7 0.4 - - - -
189C LYS* 2.8 46.2 + - - +
190C ILE* 3.3 34.0 + - + +
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Residues in contact with ALA 29 (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 ILE* 3.5 5.1 + - + +
28C VAL* 1.3 72.1 - - - +
30C GLU* 1.3 58.8 + - - +
31C ALA* 5.3 1.8 - - + -
85C THR* 2.7 19.1 + - - -
86C CYS* 2.8 40.0 + - - -
88C ILE* 4.5 5.6 - - + -
101C ILE* 3.8 27.1 - - + -
186C LEU 5.1 0.2 - - - -
187C GLU 3.3 18.4 - - - +
188C PRO* 4.1 3.4 - - + -
189C LYS 4.0 0.2 - - - +
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Residues in contact with GLU 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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28C VAL 4.4 0.4 + - - -
29C ALA* 1.3 69.1 - - - +
31C ALA* 1.3 58.7 + - - +
32C ASP 3.9 0.9 - - - -
33C PHE* 3.3 29.1 - - + -
83C GLN* 3.3 30.5 + - + +
84C ASN 3.8 10.3 - - - +
85C THR* 4.0 4.9 - - - +
185C GLY* 4.0 2.8 - - - -
186C LEU 3.1 19.4 + - - -
187C GLU* 2.8 39.3 + - + +
188C PRO 5.9 0.2 - - - -
189C LYS* 4.2 28.5 - - + +
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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