Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 2C47
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PRO* 3.8 35.0 - - + -
45A ASN* 1.3 78.8 - - - +
47A ARG* 1.3 71.0 + - - +
64A LYS 3.2 6.3 - - - +
65A ASN* 3.7 36.3 - - + -
66A LEU* 5.3 1.3 - - - +
72A VAL* 4.2 9.4 - - + -
74A ILE* 4.5 11.9 - - + -
106A TYR* 3.8 17.7 - + + -
107A TYR* 3.8 27.1 - + + -
111A CSD 4.0 18.6 - - - +
118A VAL* 3.8 35.2 - - + -
258B ASP* 4.4 9.7 - - - +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 1.3 79.2 - - - +
48A VAL* 1.3 60.2 + - - +
63A GLY* 3.1 5.5 - - - -
64A LYS* 2.9 36.6 + - + +
66A LEU* 3.9 40.0 - - + +
74A ILE* 3.8 4.2 - - - +
111A CSD 4.6 0.7 - - - -
256B LYS* 3.8 29.7 + - + +
257B ALA* 3.3 10.9 - - - +
258B ASP* 3.3 28.0 + - - +
266B LYS* 4.1 19.7 - - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 1.3 72.8 - - - +
49A GLY* 1.3 62.0 + - - +
61A ARG* 3.7 31.4 - - + -
62A LEU 3.9 2.7 - - - +
74A ILE* 4.2 14.1 - - + -
76A LEU* 4.5 9.0 - - + -
111A CSD 3.6 20.4 - - + +
256B LYS* 3.3 19.6 - - - -
257B ALA 2.9 20.5 + - - +
259B THR* 3.7 23.3 - - - -
260B LEU* 3.8 18.8 - - + +
263B ARG* 3.4 7.4 - - - -
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG 4.3 0.2 + - - -
48A VAL* 1.3 76.1 - - - +
50A LYS* 1.3 62.3 + - - -
61A ARG* 3.0 27.0 + - - -
62A LEU 2.6 18.8 + - - -
254B GLY 6.0 0.2 - - - -
255B LEU 4.1 1.3 - - - -
256B LYS* 3.9 19.8 - - - +
263B ARG* 3.4 18.1 + - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLY* 1.3 73.5 - - - -
51A LYS* 1.3 66.1 + - - +
52A ILE* 4.4 14.4 - - + -
61A ARG* 3.3 6.5 - - - +
62A LEU* 2.8 42.4 + - + +
337A PRO* 2.7 34.5 + - - +
217B ARG* 4.2 23.9 - - - +
253B GLN* 5.8 2.6 - - - +
254B GLY* 5.8 11.6 - - - +
256B LYS* 5.4 2.6 - - - +
263B ARG* 3.8 20.0 - - - +
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Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS* 1.3 82.3 - - - +
52A ILE* 1.3 67.9 + - - +
59A GLU* 4.2 16.4 - - + +
60A LEU 3.6 5.6 - - - +
61A ARG* 3.6 35.5 - - - +
167B LYS* 5.4 8.1 - - - +
214B GLY 6.0 1.1 - - - -
215B THR* 5.3 15.7 - - - +
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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