Contacts of the strand formed by residues 49 - 55 (chain C) in PDB entry 4A4C
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 VAL 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C THR* 3.8 20.2 - - + -
37C ILE 3.8 2.5 - - - -
38C MET* 3.9 26.0 - - + -
47C GLY 4.2 3.8 + - - +
48C GLY* 1.3 79.0 - - - +
50C PHE* 1.3 61.0 + - - +
51C PHE* 3.6 33.0 - - + -
71C THR* 4.2 3.6 + - - +
146C ALA* 3.6 29.9 + - - +
147C MET* 5.5 0.2 - - - +
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Residues in contact with PHE 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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35C ALA 3.7 0.2 - - - +
36C THR* 3.4 2.8 - - - +
37C ILE* 2.6 60.9 + - + +
39C GLY* 4.3 8.5 - - - -
45C TYR* 3.5 40.8 - + + -
48C GLY 4.3 10.5 - - - -
49C VAL* 1.3 73.9 - - - +
51C PHE* 1.3 61.1 + - - +
52C LEU* 4.0 1.1 - - + +
69C PHE* 3.5 25.4 - + + -
71C THR* 3.9 10.1 - - + -
72C ARG 3.9 21.5 - - - -
73C ILE* 4.0 20.2 - - + -
110C LEU* 4.5 7.0 - - + -
142C THR* 4.3 6.5 - - + -
146C ALA* 3.9 24.5 - - + -
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Residues in contact with PHE 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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34C GLN* 3.5 33.0 - - + +
35C ALA 3.1 10.8 - - - +
36C THR* 4.4 16.2 - - + -
49C VAL* 3.6 29.4 - - + -
50C PHE* 1.3 76.1 - - - +
52C LEU* 1.3 60.6 + - - +
69C PHE* 3.7 0.9 - - - -
70C THR* 2.7 40.0 + - + -
71C THR* 3.1 24.1 + - - +
146C ALA 6.0 0.4 - - - -
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Residues in contact with LEU 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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33C TRP 3.6 0.3 - - - +
34C GLN* 3.4 8.8 - - - +
35C ALA* 2.7 41.8 + - + +
37C ILE* 3.5 28.0 - - + -
50C PHE 4.0 4.3 - - - +
51C PHE* 1.3 83.1 - - - +
53C THR* 1.3 63.8 + - - +
67C VAL* 3.9 21.5 - - + -
68C ALA 3.0 19.3 - - - +
69C PHE* 3.3 41.1 - - + -
70C THR* 3.9 2.9 - - - +
103C LEU* 4.0 14.6 - - + -
106C ILE* 4.2 6.7 - - + -
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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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32C HIS* 3.1 31.9 - - + +
33C TRP 3.4 2.9 - - - +
34C GLN* 4.8 9.9 - - + +
52C LEU* 1.3 75.5 - - - +
54C ILE* 1.3 63.3 + - - +
55C HIS* 4.2 1.3 - - - -
66C LYS 3.6 1.7 - - - +
67C VAL* 3.5 4.5 - - - +
68C ALA* 2.8 43.0 + - - +
70C THR* 3.9 18.8 + - - +
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Residues in contact with ILE 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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23C ALA* 4.2 6.5 - - + -
31C PHE 3.3 6.1 - - - +
32C HIS* 3.4 3.8 - - - -
33C TRP* 2.9 51.1 + - + +
35C ALA* 3.7 28.9 - - + -
52C LEU 5.3 0.2 - - - -
53C THR* 1.3 78.3 - - - +
55C HIS* 1.3 61.6 + - - +
56C PHE* 3.7 28.9 - - + -
65C PRO* 4.0 20.6 - - + -
66C LYS 3.4 3.8 - - - +
67C VAL* 4.0 19.7 - - + -
99C ILE* 4.7 15.3 - - + -
103C LEU* 5.0 4.3 - - + -
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Residues in contact with HIS 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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31C PHE* 3.3 16.5 + + + +
32C HIS* 4.9 4.5 - - + +
53C THR* 4.2 1.5 - - - -
54C ILE* 1.3 74.7 - - - +
56C PHE* 1.3 84.6 + - - +
57C PRO* 3.5 12.0 - - + +
58C THR* 5.5 1.8 - - + -
65C PRO* 3.6 0.6 - - - +
66C LYS* 2.8 66.6 + - + +
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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