Contacts of the strand formed by residues 43 - 51 (chain C) in PDB entry 3T30
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 ARG 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C SER* 5.9 3.4 - - - -
42C CYS* 1.3 90.9 - - - +
44C LEU* 1.3 61.4 + - - +
45C LEU* 3.4 19.1 + - + -
97C GLN* 3.5 37.0 + - + +
98C LEU 3.4 9.1 + - - +
99C SER* 3.4 24.3 + - - -
118C GLN 3.6 0.2 - - - +
119C GLU* 3.7 1.7 - - - -
120C ARG* 3.0 50.1 + - + +
121C TYR* 6.2 0.9 - - + -
16D THR* 4.3 16.6 + - - +
118D GLN* 4.7 2.4 + - - +
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Residues in contact with LEU 44 (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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19C TRP* 4.0 33.7 - - + -
32C PHE* 3.8 29.5 - - + -
43C ARG* 1.3 71.6 - - - +
45C LEU* 1.3 78.2 + - - +
46C LEU* 3.5 17.3 + - + +
97C GLN* 3.5 0.2 - - - -
98C LEU* 2.9 44.3 + - + +
100C PRO* 4.8 0.2 - - - +
102C VAL* 3.6 29.4 - - + -
104C PHE* 3.6 18.8 - - + -
118C GLN 3.8 6.1 - - - +
119C GLU* 4.9 1.1 - - + +
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Residues in contact with LEU 45 (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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16C THR* 5.9 1.8 - - + -
43C ARG* 4.0 16.8 - - + +
44C LEU* 1.3 75.8 - - - +
46C LEU* 1.3 59.2 + - - +
47C HIS* 3.9 16.2 - - + +
95C GLY 6.3 0.4 - - - +
96C VAL 3.5 5.8 - - - +
97C GLN* 3.6 35.0 - - + +
117C GLY* 2.9 7.1 - - - -
118C GLN* 2.8 62.4 + - + +
120C ARG* 4.2 35.4 - - + +
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Residues in contact with LEU 46 (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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19C TRP* 4.1 18.2 - - + -
44C LEU* 3.5 11.0 + - + -
45C LEU* 1.3 70.4 - - - +
47C HIS* 1.3 60.8 + - - +
48C THR 4.6 4.5 - - - +
49C ILE* 4.3 4.7 - - + -
64C ILE* 5.4 0.2 - - + -
80C ILE* 3.9 23.8 - - + -
93C MET* 3.0 52.9 - - + +
94C VAL* 4.0 0.7 + - - -
96C VAL* 3.0 28.2 + - + +
98C LEU* 4.4 9.6 - - + -
104C PHE* 4.3 9.2 - - + -
115C LEU* 4.3 17.5 - - + -
116C SER 3.7 13.9 - - - +
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Residues in contact with HIS 47 (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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95B GLY 5.1 1.0 + - - -
96B VAL* 3.8 36.7 - - + +
98B LEU* 6.1 0.2 - - - +
18C LEU* 5.6 2.0 - - - +
45C LEU* 3.7 18.3 + - + +
46C LEU* 1.3 79.1 - - - +
48C THR* 1.3 69.3 + - + +
92C SER* 3.5 0.3 - - - -
93C MET* 2.7 30.1 + - - -
94C VAL* 3.6 26.7 + - + +
95C GLY 4.9 2.0 - - - -
116C SER* 2.8 21.4 + - - +
117C GLY* 3.7 11.3 + - - -
118C GLN* 2.8 44.3 + - + -
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Residues in contact with THR 48 (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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79B THR 3.9 0.2 + - - -
80B ILE* 3.0 29.3 + - + +
93B MET* 3.9 25.1 - - + -
46C LEU* 4.1 1.3 - - - +
47C HIS* 1.3 90.5 - - + +
49C ILE* 1.3 70.6 + - - +
50C CYS* 3.9 4.3 - - - -
90C MET* 3.9 11.0 - - + -
91C VAL 3.3 9.9 - - - +
92C SER* 4.1 8.3 - - - +
93C MET* 5.3 0.7 - - - -
114C PHE 4.0 0.2 - - - +
115C LEU* 3.5 0.3 - - - +
116C SER* 2.5 50.6 + - - +
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Residues in contact with ILE 49 (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* 4.3 7.9 - - + -
48C THR* 1.3 80.3 - - - +
50C CYS* 1.3 63.2 + - - +
62C VAL* 4.5 17.9 - - + -
80C ILE* 3.9 25.4 - - + -
81C ALA* 3.8 21.8 - - + -
83C LEU* 3.4 18.6 - - + +
90C MET* 3.1 3.8 - - - +
91C VAL* 3.0 38.4 + - + -
93C MET* 4.1 16.2 - - + -
113C VAL* 5.0 7.0 - - + -
114C PHE 3.1 11.0 - - - +
115C LEU* 4.1 24.7 - - + -
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Residues in contact with CYS 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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79B THR* 3.9 16.6 - - + -
80B ILE 3.6 25.6 - - - -
81B ALA* 3.6 16.8 - - - -
82B SER* 3.2 20.2 - - - +
48C THR* 3.9 7.6 - - - -
49C ILE* 1.3 81.3 - - - +
51C LEU* 1.3 62.1 + - - +
83C LEU* 4.4 2.5 - - - -
89C PRO 3.5 5.4 - - - -
90C MET* 3.8 11.9 - - - -
113C VAL* 3.6 0.4 - - - -
114C PHE* 2.8 38.9 + - - +
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Residues in contact with LEU 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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59B MET* 3.4 5.2 - - - +
82B SER* 2.8 25.1 + - - -
50C CYS* 1.3 73.2 - - - +
52C GLY* 1.3 68.9 + - - +
55C ALA* 4.3 5.8 - - + -
60C HIS* 3.7 29.8 - - + +
83C LEU* 4.1 12.3 - - + +
84C GLN* 3.6 16.4 - - - +
85C ALA* 3.2 40.6 - - + +
89C PRO* 2.8 24.8 + - + +
112C PRO 3.9 2.7 - - - +
113C VAL* 3.7 28.3 - - + -
114C PHE* 4.5 1.1 - - - -
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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