Contacts of the strand formed by residues 37 - 44 (chain C) in PDB entry 2OTD
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 MSE 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C TYR* 3.5 34.5 - - + -
7C PRO* 3.4 36.1 - - + +
9C ILE 4.0 8.0 + - - +
10C VAL* 3.5 26.5 - - + -
11C ALA* 3.0 23.2 + - - +
35C HIS* 3.5 4.4 - - - +
36C LYS* 1.3 83.4 - - - +
38C ILE* 1.3 70.7 + - - +
109C MSE 4.3 1.1 - - - +
110C MSE 3.2 16.6 - - + +
111C ALA 4.1 4.0 - - - +
112C ASN* 3.8 31.6 - - + +
144C LEU* 4.2 9.9 - - + -
211C LEU* 5.8 0.7 - - + -
231C CYS* 5.3 2.0 - - - -
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Residues in contact with ILE 38 (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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10C VAL* 3.6 4.7 - - - +
11C ALA* 3.6 8.7 - - + +
14C GLY* 4.0 24.9 - - - +
27C ILE* 3.6 37.5 - - + -
37C MSE 1.3 79.8 - - - +
39C GLU* 1.3 60.6 + - - +
40C PHE* 3.8 18.5 - - + -
104C CYS* 3.5 24.9 - - - -
109C MSE 3.7 29.2 - - + -
110C MSE 3.0 14.4 + - - +
111C ALA* 3.5 0.7 - - - -
112C ASN 2.9 24.3 + - - +
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Residues in contact with GLU 39 (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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10C VAL* 3.5 15.0 - - + +
11C ALA 3.0 10.8 + - - +
12C HIS* 3.1 26.8 - - + -
13C ARG* 2.8 33.4 + - - +
14C GLY 3.2 4.2 + - - -
38C ILE* 1.3 74.7 - - - +
40C PHE* 1.3 76.2 + - - +
41C ASP* 2.9 22.9 - - - +
112C ASN* 3.3 31.2 - - - +
114C GLU* 3.2 20.5 - - + +
211C LEU* 6.2 0.7 - - + -
233C CYS* 4.6 6.7 - - - -
301D PO4 3.3 15.9 + - - +
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Residues in contact with PHE 40 (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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13C ARG* 4.6 2.7 - - - -
14C GLY 5.1 0.2 - - - +
22C ASN* 3.4 17.3 - - - +
27C ILE* 5.1 2.0 - - + -
38C ILE* 3.8 28.7 - - + -
39C GLU* 1.3 91.1 - - - +
41C ASP* 1.3 59.4 + - - +
42C ALA* 3.8 0.6 + - + -
52C LEU* 3.7 28.9 - - + -
97C LEU* 3.6 24.0 - - + -
100C VAL* 3.4 24.5 - - + -
111C ALA* 4.0 13.9 - - + -
112C ASN 3.1 6.5 + - - +
113C ILE* 3.8 27.5 - - + -
114C GLU 3.0 23.0 + - - +
137C TRP* 4.1 10.5 - + - -
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Residues in contact with ASP 41 (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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13C ARG* 3.2 20.5 + - - -
22C ASN* 2.7 27.7 - - - +
39C GLU* 2.9 22.0 - - - +
40C PHE* 1.3 72.7 - - - +
42C ALA* 1.3 59.0 + - - +
52C LEU* 3.0 26.6 - - - +
53C LEU 3.0 5.7 + - - -
54C HIS* 3.4 29.8 - - - +
114C GLU* 3.1 20.9 - - - +
116C LYS* 4.0 10.5 - - + -
301D PO4 3.4 5.7 + - - -
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C PHE* 3.8 1.3 + - + +
41C ASP* 1.3 73.7 - - - +
43C LYS* 1.3 62.1 + - - +
50C ILE* 4.0 19.7 - - + -
51C PHE 3.5 5.6 - - - +
52C LEU* 4.3 10.1 - - + +
97C LEU* 4.7 3.1 - - + -
113C ILE* 4.0 24.7 - - + -
114C GLU 2.9 11.0 + - - +
115C ILE* 3.8 2.3 - - - -
116C LYS 2.8 33.1 + - - +
117C PRO 4.2 0.2 - - - -
125C THR* 4.4 2.6 - - - +
129C VAL* 4.3 9.0 - - + -
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C ALA* 1.3 69.2 - - - +
44C LEU* 1.3 67.5 + - - +
49C GLU 3.4 0.2 - - - +
50C ILE* 3.3 8.1 - - - +
51C PHE* 3.0 49.7 + - + +
53C LEU* 2.9 30.8 + - + +
54C HIS 2.8 27.1 + - - -
55C ASP 3.1 21.9 - - - +
56C ASP* 4.1 8.1 - - - +
68C ALA* 5.1 2.2 - - + -
69C GLY 5.5 0.2 - - - +
116C LYS* 2.7 36.9 + - - +
117C PRO 4.3 1.0 + - - -
118C THR* 3.9 27.6 - - - +
125C THR* 4.3 7.9 - - - -
129C VAL* 4.8 0.2 - - - +
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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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43C LYS* 1.3 81.3 - - - +
45C SER* 1.3 68.8 + - - +
48C GLY* 4.5 1.3 - - - -
49C GLU 3.3 3.1 - - - +
50C ILE* 4.0 27.1 - - + -
51C PHE* 3.5 8.4 - - - -
69C GLY* 3.5 19.8 - - - +
118C THR* 4.4 6.5 + - - +
121C THR* 5.6 3.4 - - - +
124C LEU* 3.8 11.7 - - + -
125C THR* 3.4 45.4 + - + +
128C MSE 3.0 41.5 - - + -
129C VAL* 4.7 1.8 - - + -
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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