Contacts of the strand formed by residues 18 - 26 (chain A) in PDB entry 2MF1
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 ILE 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 3.3 8.9 - - - +
14A ILE* 2.9 53.4 + - + +
15A GLY* 5.7 0.7 - - - -
17A ASP* 1.3 102.8 - - - +
19A THR* 1.3 68.4 + - - +
20A ILE* 3.8 24.0 - - + -
34A ILE* 4.8 0.2 - - + -
35A ASN 3.6 2.9 - - - -
36A ALA* 3.8 24.0 - - + -
37A PRO* 4.5 0.2 - - + -
40A VAL* 4.6 6.5 - - + -
14B ILE* 3.8 32.3 - - + -
18B ILE* 4.7 8.5 - - + -
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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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11A SER* 4.5 4.5 - - - -
12A ILE 3.2 19.7 - - - +
13A ASN* 3.6 9.9 + - - +
17A ASP 4.9 2.1 + - - -
18A ILE* 1.3 76.4 + - - +
20A ILE* 1.3 69.0 + - - +
21A THR* 5.1 3.1 - - - +
35A ASN* 2.7 58.1 + - - +
45B GLU* 3.8 25.8 - - + +
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Residues in contact with ILE 20 (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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11A SER* 3.1 7.6 - - - -
12A ILE* 2.8 51.1 + - + +
14A ILE* 4.0 19.7 - - + -
18A ILE* 3.8 8.3 - - + -
19A THR* 1.3 84.2 - - - +
21A THR* 1.3 65.9 + - - +
32A ILE* 3.6 21.5 - - + -
33A GLY 3.5 10.8 - - - +
34A ILE* 3.9 16.4 - - + -
14B ILE* 3.8 28.9 - - + -
20B ILE* 5.7 6.7 - - + -
32B ILE* 6.2 3.1 - - + -
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Residues in contact with THR 21 (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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9A GLY 4.8 3.8 - - - +
10A GLU 3.7 8.3 - - - +
11A SER* 3.6 17.5 + - - +
19A THR* 5.1 3.6 - - - +
20A ILE* 1.3 76.9 + - - +
22A ILE* 1.3 63.4 + - - +
23A LEU* 3.2 18.1 + - + +
32A ILE* 3.5 5.9 - - - +
33A GLY 2.8 40.7 + - - +
35A ASN* 5.6 2.1 - - - +
1B MET* 4.2 12.4 - - - +
52G A 3.7 34.5 + - + +
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Residues in contact with ILE 22 (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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6A ARG* 3.8 17.3 - - + +
7A LYS 3.1 26.5 - - - +
8A VAL* 3.9 15.0 - - + -
9A GLY* 2.9 32.4 + - - -
10A GLU 3.2 15.7 + - - +
21A THR* 1.3 71.4 - - - +
23A LEU* 1.3 57.7 + - - +
24A GLY 3.2 27.8 - - - +
30A VAL* 3.2 28.5 - - + -
31A ARG 3.6 5.4 - - - +
32A ILE* 4.2 6.7 - - + +
30B VAL* 4.1 19.5 - - + -
32B ILE* 5.7 5.8 - - + -
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Residues in contact with LEU 23 (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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8A VAL* 4.0 8.1 - - - +
9A GLY* 4.8 1.4 + - - -
21A THR* 3.5 27.1 - - - +
22A ILE* 1.3 73.4 - - - +
24A GLY* 1.3 55.4 + - - +
31A ARG* 2.9 26.1 + - + +
33A GLY* 3.7 11.4 - - - +
1B MET* 4.1 3.6 - - + -
3B ILE* 3.6 47.6 - - + -
52G A 3.5 47.8 - - + +
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Residues in contact with GLY 24 (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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8A VAL* 3.7 20.2 - - - -
22A ILE* 3.2 13.3 - - - +
23A LEU* 1.3 80.4 - - - +
25A VAL* 1.3 59.2 + - - -
31A ARG* 2.8 33.4 + - - +
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Residues in contact with VAL 25 (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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8A VAL* 3.7 20.8 - - + +
24A GLY* 1.3 73.5 - - - +
26A SER* 1.3 68.5 + - - +
27A GLY 3.9 15.3 - - - +
29A GLN 3.5 13.7 - - - +
30A VAL* 4.3 6.3 - - + +
31A ARG 4.6 0.4 - - - +
25B VAL* 4.1 21.3 - - + -
27B GLY 4.4 4.7 - - - +
28B GLN* 3.5 33.4 - - + +
30B VAL* 4.8 8.3 - - + -
44G U 5.4 0.2 + - - -
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Residues in contact with SER 26 (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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25A VAL* 1.3 74.8 + - - +
27A GLY* 1.3 61.9 + - - +
28A GLN 3.3 3.5 + - - -
29A GLN* 2.9 43.2 + - - +
30A VAL* 4.8 0.4 - - - +
31A ARG* 5.6 6.2 - - - +
5B THR* 5.9 1.3 - - - -
44G U 3.9 32.4 + - - +
45G C 3.6 8.4 + - - -
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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