Contacts of the strand formed by residues 49 - 56 (chain C) in PDB entry 2CFX
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 ILE 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ILE* 4.9 4.0 - - + -
14C LEU* 4.1 19.3 - - + -
40C VAL* 4.7 4.9 - - + -
43C LEU* 3.3 34.9 + - + -
44C GLU* 3.9 29.1 - - + +
47C GLY* 4.1 3.7 - - - -
48C ILE* 1.3 79.3 - - + +
50C LYS* 1.3 64.3 + - - +
51C GLN 4.1 7.9 - - - +
52C TYR* 3.6 35.9 - - + +
54H LEU* 3.8 35.7 - - + -
55H GLU 3.5 4.0 - - - +
56H VAL* 4.6 1.3 - - + +
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Residues in contact with LYS 50 (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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47C GLY* 4.2 6.1 - - - +
48C ILE 3.7 0.2 + - - -
49C ILE* 1.3 73.6 - - - +
51C GLN* 1.3 62.4 + - + +
55H GLU* 2.5 43.9 + - + +
56H VAL 3.3 19.8 + - - -
57H ASP* 4.0 33.4 - - + +
136H GLU* 5.7 4.1 + - - -
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Residues in contact with GLN 51 (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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49C ILE* 3.5 3.7 - - - -
50C LYS* 1.3 85.8 - - + +
52C TYR* 1.3 77.5 + - - +
53C THR* 3.6 17.2 + - - -
15H LYS 3.8 9.8 - - - +
16H LYS* 2.9 29.2 + - - +
54H LEU* 3.5 2.6 - - - +
55H GLU* 2.6 53.0 + - + +
140H LYS* 5.7 5.0 - - - +
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Residues in contact with TYR 52 (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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14C LEU* 4.3 12.5 - - + +
18C SER* 3.7 15.7 - - - +
40C VAL* 3.6 10.6 - - - +
44C GLU* 2.5 31.1 + - + -
49C ILE* 3.6 29.4 - - + +
51C GLN* 1.3 74.3 - - - +
53C THR* 1.3 62.2 + - - +
16H LYS 3.7 6.0 + - - +
17H ASP* 3.4 14.9 + - - +
18H SER* 3.0 28.5 + - - +
19H ARG* 3.4 50.6 + - + -
53H THR 3.8 2.9 - - - -
54H LEU* 3.4 26.2 - - + +
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Residues in contact with THR 53 (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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51C GLN* 3.6 20.0 + - - -
52C TYR* 1.3 76.5 - - - +
54C LEU* 1.3 65.7 + - - +
14H LEU 4.2 0.4 - - - -
15H LYS* 3.1 21.8 + - - +
18H SER* 2.7 25.9 + - - -
53H THR* 2.8 56.7 + - + -
54H LEU 4.0 11.7 - - - +
55H GLU* 4.1 15.3 + - + +
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Residues in contact with LEU 54 (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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53C THR* 1.3 86.5 + - - +
55C GLU* 1.3 67.2 + - - +
56C VAL* 4.0 14.6 - - + -
11H ILE* 3.7 25.6 - - - +
14H LEU* 4.2 13.7 - - + +
15H LYS* 3.7 39.0 + - + +
49H ILE* 4.0 24.2 - - + -
51H GLN 3.5 10.1 - - - +
52H TYR* 3.5 38.6 - - + -
53H THR* 4.1 4.1 - - - +
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Residues in contact with GLU 55 (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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54C LEU* 1.3 76.4 - - - +
56C VAL* 1.3 60.6 + - - +
15H LYS* 5.0 1.3 - - - +
49H ILE* 3.7 3.3 - - - -
50H LYS* 2.8 64.9 + - + +
51H GLN* 2.9 39.9 + - + +
53H THR* 4.5 12.8 + - + +
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Residues in contact with VAL 56 (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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54C LEU* 4.0 18.8 - - + -
55C GLU* 1.3 81.4 - - - +
57C ASP* 1.3 69.4 + - - +
58C GLN* 3.2 21.5 + - - +
61C LEU* 2.9 35.9 - - + -
11H ILE* 4.0 16.4 - - + -
15H LYS* 3.7 31.4 - - - +
48H ILE* 3.4 8.7 - - + +
49H ILE* 5.1 0.7 - - - -
50H LYS* 3.6 14.0 + - - -
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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