Contacts of the strand formed by residues 18 - 26 (chain C) in PDB entry 2MF0
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASN* 2.9 11.0 + - - +
14C ILE* 2.9 58.2 + - + +
15C GLY* 4.9 3.4 - - - +
16C ASP 3.9 0.6 - - - -
17C ASP* 1.3 94.3 - - + +
19C THR* 1.3 65.6 + - - +
20C ILE* 3.9 25.6 - - + -
34C ILE* 4.8 2.5 - - + -
35C ASN 3.3 9.4 - - - +
36C ALA* 3.6 25.1 - - + -
37C PRO* 4.4 2.5 - - + -
40C VAL* 4.8 12.8 - - + -
14D ILE* 4.9 11.7 - - + -
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Residues in contact with THR 19 (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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11C SER* 4.8 9.0 - - - +
12C ILE 3.4 13.5 - - - +
13C ASN* 3.0 19.1 + - - +
17C ASP 4.3 0.5 + - - -
18C ILE* 1.3 72.0 - - - +
20C ILE* 1.3 70.9 + - - +
21C THR* 4.4 9.2 - - - +
33C GLY 4.3 0.2 - - - +
35C ASN* 2.8 53.3 + - + +
1D MET* 5.1 0.2 - - - +
45D GLU* 5.7 1.6 - - + -
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Residues in contact with ILE 20 (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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11C SER* 3.5 2.4 - - - -
12C ILE* 2.8 55.2 + - + +
14C ILE* 3.8 25.8 - - + -
18C ILE* 3.9 9.4 - - + -
19C THR* 1.3 80.5 - - - +
21C THR* 1.3 68.0 + - - +
32C ILE* 4.1 17.9 - - + -
33C GLY 3.5 8.1 - - - +
34C ILE* 3.7 30.5 - - + -
14D ILE* 4.0 13.5 - - + -
20D ILE* 5.8 7.2 - - + -
32D ILE* 5.6 9.4 - - + -
34D ILE* 6.3 0.7 - - + -
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Residues in contact with THR 21 (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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9C GLY 4.5 3.4 - - - +
10C GLU 3.5 14.4 - - - +
11C SER* 3.8 11.4 + - - +
19C THR* 4.4 8.5 - - - +
20C ILE* 1.3 78.6 + - - +
22C ILE* 1.3 67.0 + - - +
23C LEU* 3.4 21.8 - - + +
32C ILE* 3.6 6.4 - - - +
33C GLY 2.8 38.5 + - - -
1D MET* 4.2 16.3 - - - +
67G C 3.7 24.3 + - + +
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Residues in contact with ILE 22 (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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6C ARG* 3.3 27.0 - - + +
7C LYS 3.2 25.8 - - - +
8C VAL* 4.1 11.4 - - + -
9C GLY* 2.8 29.7 + - - +
10C GLU 3.2 7.9 + - - +
21C THR* 1.3 74.0 - - - +
23C LEU* 1.3 59.0 + - - +
24C GLY 3.9 8.5 - - - +
30C VAL* 3.3 34.3 - - + -
31C ARG 3.6 13.9 - - - +
32C ILE* 4.6 5.8 - - + -
30D VAL* 3.8 24.0 - - + -
32D ILE* 4.5 12.7 - - + +
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Residues in contact with LEU 23 (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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8C VAL* 4.3 2.8 - - - +
9C GLY* 4.2 9.6 + - - -
21C THR* 3.4 35.2 - - + +
22C ILE* 1.3 74.1 - - - +
24C GLY* 1.3 60.3 + - - +
31C ARG* 2.8 25.1 + - + +
33C GLY* 3.7 11.7 - - - +
1D MET* 4.6 0.2 - - + -
3D ILE* 3.5 31.4 - - + -
67G C 3.7 32.0 - - + +
68G G 3.3 27.8 - - - +
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Residues in contact with GLY 24 (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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8C VAL* 3.6 17.7 - - - -
22C ILE* 3.7 4.7 - - - +
23C LEU* 1.3 81.7 - - - +
25C VAL* 1.3 63.4 + - - +
30C VAL* 3.5 3.6 - - - -
31C ARG* 2.8 33.2 + - - +
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Residues in contact with VAL 25 (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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8C VAL* 3.9 13.1 - - + +
24C GLY* 1.3 78.3 - - - +
26C SER* 1.3 65.5 + - - +
27C GLY 4.5 11.0 - - - +
29C GLN 3.3 9.9 - - - +
30C VAL* 4.4 3.6 - - + -
31C ARG 5.6 0.2 - - - -
25D VAL* 4.1 19.3 - - + -
27D GLY 4.6 13.9 - - - +
28D GLN* 5.2 1.8 - - + +
29D GLN 5.0 1.6 - - - +
30D VAL* 3.8 27.4 - - + -
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Residues in contact with SER 26 (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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25C VAL* 1.3 75.8 - - - +
27C GLY* 1.3 58.3 + - - +
29C GLN* 2.8 37.4 + - - +
31C ARG 5.6 0.2 - - - +
5D THR* 6.5 0.4 - - - -
59G C 2.9 30.6 + - - -
60G A 3.8 20.2 + - - +
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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