Contacts of the strand formed by residues 31 - 34 (chain C) in PDB entry 2FBE
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 31 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.2 5.4 - - - -
25C ILE* 3.2 6.2 - - - +
26C SER* 3.1 37.5 + - - -
28C ASP* 4.5 3.5 + - - -
30C ARG* 1.3 83.5 + - - +
32C PHE* 1.3 65.6 + - - +
180C ILE* 3.9 13.8 - - - +
181C LEU 3.1 9.2 - - - -
182C SER* 3.1 16.4 - - - -
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.6 22.4 - + + -
23C LEU* 3.9 30.1 - - + -
24C ILE 3.3 13.0 - - - +
25C ILE* 4.1 14.8 - - + -
31C SER* 1.3 77.7 - - - +
33C ARG* 1.3 67.1 + - - +
54C VAL* 3.5 27.4 - - + -
168C PHE* 3.7 11.2 - - + -
169C ALA 4.4 5.4 - - - -
170C HIS* 3.7 31.4 - + + -
179C SER 4.1 0.3 - - - +
180C ILE* 3.8 4.3 - - - +
181C LEU* 2.8 68.3 + - + +
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Residues in contact with ARG 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.4 3.6 - - - -
24C ILE* 3.0 74.8 + - + +
32C PHE* 1.3 78.7 - - - +
34C SER* 1.3 64.1 + - - +
35C GLY* 3.7 2.8 + - - -
170C HIS* 4.5 1.8 - - - -
176C ASP* 5.5 7.1 + - - -
177C ASP 3.6 19.5 - - - +
178C GLN* 4.7 2.6 - - - +
179C SER 3.2 21.8 - - - +
180C ILE* 3.7 17.7 - - + +
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Residues in contact with SER 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR 3.9 3.8 - - - -
23C LEU* 3.3 18.3 - - - +
33C ARG* 1.3 74.1 - - - +
35C GLY* 1.3 61.2 + - - +
36C ASP* 4.9 0.2 - - - +
52C LEU* 4.3 6.5 - - - -
170C HIS* 2.6 43.8 + - - -
172C ARG* 3.6 34.3 - - - +
177C ASP* 3.9 19.9 + - - +
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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
------------------------------------------------------------
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