Contacts of the strand formed by residues 12 - 19 (chain A) in PDB entry 3UMO
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 SER 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 5.1 0.9 - - - -
11A PRO* 1.3 78.2 - - - +
13A LEU* 1.3 59.7 + - - +
14A ASP* 2.7 28.5 + - - -
38A GLY* 2.8 38.7 + - - +
39A GLY* 4.1 1.2 + - - -
69A LEU* 3.6 9.8 - - - +
89A THR* 3.9 6.7 - - - -
90A ARG* 3.2 17.9 - - - -
92A ASN* 3.7 18.5 + - - -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 1.3 69.9 - - - +
14A ASP* 1.3 60.5 + - - +
35A PHE* 4.0 10.3 - - + -
36A GLU 3.9 4.5 - - - +
65A THR* 3.7 39.3 - - + +
68A HIS* 3.9 9.2 - - + -
69A LEU* 3.9 19.7 - - + +
72A LEU* 3.8 30.1 - - + -
89A THR* 3.7 7.4 - - + +
90A ARG 2.9 10.4 + - - +
91A GLN* 3.0 38.5 + - + +
88B TRP* 3.9 27.6 - - + -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A SER* 2.7 24.2 + - - -
13A LEU* 1.3 74.1 - - - +
15A SER* 1.3 62.3 + - - +
16A ALA 4.1 0.4 + - - -
34A VAL 3.6 0.7 - - - +
35A PHE* 3.2 7.6 - - - -
36A GLU* 2.8 56.2 + - + +
37A PRO 4.3 1.7 - - - +
38A GLY* 3.4 20.2 - - - -
39A GLY 4.9 0.2 + - - -
92A ASN* 3.2 33.8 + - - +
94A HIS* 5.9 2.9 - - + +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 3.8 0.4 + - - -
14A ASP* 1.3 73.1 - - - +
16A ALA* 1.3 58.0 + - - +
17A THR 4.0 0.4 - - - -
33A PRO* 3.6 18.5 - - - +
34A VAL 3.7 3.4 - - - -
35A PHE* 3.2 13.7 - - - -
36A GLU* 5.9 0.9 - - - -
91A GLN* 3.0 24.3 + - - +
92A ASN 2.9 9.2 + - - -
93A LEU* 3.5 19.7 - - - +
94A HIS* 2.8 27.7 + - - +
108B MET* 4.7 3.3 - - - -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP 4.1 0.2 + - - -
15A SER* 1.3 72.3 - - - +
17A THR* 1.3 60.0 + - - +
18A ILE* 5.8 0.4 - - - +
32A ALA 4.5 0.9 - - - +
33A PRO* 3.3 3.0 - - - +
34A VAL* 2.8 52.6 + - + +
36A GLU* 4.4 16.6 + - - +
94A HIS* 3.4 23.6 - - + +
292A THR* 5.9 0.9 - - + +
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER 4.0 0.2 - - - -
16A ALA* 1.3 74.4 - - - +
18A ILE* 1.3 74.4 + - - +
30A CYS* 3.1 21.2 - - + +
31A THR* 2.6 38.1 + - - -
33A PRO* 4.5 0.9 - - - -
93A LEU* 3.9 19.7 - - + -
94A HIS* 2.9 15.6 + - - +
95A VAL* 4.0 14.4 - - + -
96A HIS* 2.9 25.8 + - - +
108B MET* 4.1 10.5 - - - -
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 5.8 0.4 - - - +
17A THR* 1.3 85.7 + - - +
19A THR* 1.3 65.1 + - - +
29A ARG 3.9 0.3 - - - +
30A CYS* 3.3 4.7 - - - -
31A THR* 2.9 48.8 + - + +
96A HIS* 3.4 22.0 - - + +
98A GLU* 3.4 38.8 - - + +
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Residues in contact with THR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 1.3 75.0 - - - +
20A PRO* 1.3 71.7 - - - +
21A GLN 3.4 21.9 + - - +
22A ILE* 5.3 1.1 - - + -
28A LEU* 4.0 13.6 - - + +
29A ARG 2.8 27.8 + - - -
30A CYS* 3.9 12.6 - - - -
95A VAL* 3.8 22.0 - - + +
96A HIS 3.0 9.1 + - - +
97A VAL* 3.4 6.6 - - + -
98A GLU* 2.9 26.8 + - - +
106B PHE* 5.3 0.2 - - + -
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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