Contacts of the strand formed by residues 53 - 59 (chain C) in PDB entry 2AFG
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 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ALA* 3.4 2.3 - - - -
49C GLU* 3.0 27.7 + - - +
50C SER* 2.9 32.0 + - - +
51C VAL 3.5 2.9 - - - +
52C GLY* 1.3 76.8 - - - +
54C VAL* 1.3 65.4 + - - +
84C LEU* 3.9 23.5 - - + +
85C PHE 3.0 6.5 - - - +
86C LEU* 3.5 23.8 - - + +
100C LYS* 3.7 27.3 + - + +
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Residues in contact with VAL 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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46C LEU* 4.6 12.1 - - + -
47C SER 2.8 12.6 - - - +
48C ALA* 4.5 11.7 - - + -
52C GLY 5.0 0.2 - - - -
53C GLU* 1.3 80.5 - - - +
55C TYR* 1.3 66.2 + - - +
56C ILE* 3.9 23.3 - - + -
83C CYS 3.9 0.5 - - - +
84C LEU* 3.5 9.8 - - - +
85C PHE* 2.9 34.9 + - + +
87C GLU* 4.1 29.4 - - + +
97C TYR* 4.0 18.2 - - + -
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Residues in contact with TYR 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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45C GLN 3.3 5.7 - - - +
46C LEU* 3.3 4.5 - - - +
47C SER* 2.6 45.1 + - - +
49C GLU* 2.8 42.2 + - + -
54C VAL* 1.3 73.6 - - - +
56C ILE* 1.3 63.3 + - - +
57C LYS* 4.0 1.1 - - + -
64C TYR* 3.7 31.9 - + + -
79C PRO* 4.3 17.2 - - + +
80C ASN* 4.5 4.7 + - - -
83C CYS* 3.3 36.6 - - + -
84C LEU* 3.4 33.0 - - + +
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Residues in contact with ILE 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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14C LEU* 5.2 5.6 - - + -
23C LEU* 5.4 2.9 - - + -
25C ILE* 4.4 1.9 - - + +
44C LEU* 4.2 31.4 - - + -
45C GLN 3.8 2.5 - - - -
46C LEU* 3.9 18.4 - - + -
54C VAL* 3.9 23.6 - - + -
55C TYR* 1.3 78.5 - - - +
57C LYS* 1.3 57.6 + - - +
64C TYR* 3.2 2.9 - - - -
65C LEU* 2.6 65.1 + - + +
83C CYS 4.8 3.6 + - - -
85C PHE* 4.2 18.8 - - + -
97C TYR* 4.2 20.4 - - + -
109C VAL* 6.2 0.2 - - + -
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Residues in contact with LYS 57 (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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44C LEU* 3.7 6.8 - - - -
45C GLN* 3.3 57.4 + - + +
55C TYR* 4.0 1.7 - - + -
56C ILE* 1.3 76.4 - - - +
58C SER* 1.3 73.5 + - - +
59C THR* 3.4 4.7 + - - +
62C GLY* 4.0 20.7 + - - +
63C GLN 2.9 17.0 - - - +
64C TYR* 3.9 32.4 + - + +
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Residues in contact with SER 58 (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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25C ILE* 4.2 26.3 + - - +
41C HIS* 5.1 6.6 - - - -
43C GLN 3.9 8.7 - - - -
44C LEU* 4.4 4.5 - - - -
57C LYS* 1.3 76.0 - - - +
59C THR* 1.3 57.4 + - - +
60C GLU* 3.1 7.5 + - - +
61C THR* 2.9 35.3 + - - +
62C GLY* 2.9 26.3 + - - -
63C GLN 2.5 14.5 + - - -
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Residues in contact with THR 59 (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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11C PRO* 4.5 14.8 - - + -
43C GLN* 3.2 32.5 + - - +
44C LEU 4.0 10.1 - - - +
45C GLN* 3.9 32.8 - - + +
57C LYS* 3.4 9.4 + - - +
58C SER* 1.3 71.8 - - - +
60C GLU* 1.3 67.7 + - - +
62C GLY* 4.4 2.1 + - - -
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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