Contacts of the strand formed by residues 5 - 12 (chain C) in PDB entry 1MF8
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 THR 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ASN 3.8 5.7 + - - -
4C PRO* 1.3 76.2 + - - +
6C VAL* 1.3 57.1 + - - +
21C SER* 4.2 6.5 - - - -
22C PHE 3.4 8.2 + - - +
23C GLU* 4.9 1.0 - - - -
133C LYS* 3.0 44.8 + - + +
163C GLN* 4.5 3.4 - - - +
164C LEU* 2.5 67.1 + - + +
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Residues in contact with VAL 6 (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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4C PRO 5.1 0.2 - - - -
5C THR* 1.3 77.6 - - - +
7C PHE* 1.3 82.9 + - - +
8C PHE* 4.1 8.1 - - + -
21C SER* 3.1 10.0 - - - -
22C PHE* 3.1 32.5 + - + +
24C LEU* 4.1 25.6 - - + -
36C PHE* 4.5 7.4 - - + -
37C ARG* 4.3 13.0 - - + +
40C SER* 3.2 37.7 - - - +
162C GLY 2.9 19.1 - - - +
163C GLN* 4.2 5.8 - - + +
164C LEU* 3.8 0.9 - - - +
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Residues in contact with PHE 7 (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 VAL* 1.3 83.8 - - - +
8C PHE* 1.3 78.0 + - - +
9C ASP* 2.8 25.6 - - - -
19C ARG* 3.0 50.9 - - + -
20C VAL 3.2 8.1 - - - +
21C SER* 4.3 1.6 - - - -
22C PHE* 4.6 0.2 - - - -
160C ASP* 3.1 22.4 - - - -
161C CYS* 3.2 23.3 - - - +
162C GLY* 3.0 45.4 + - - -
163C GLN 4.2 5.4 - - - -
164C LEU* 3.8 19.5 - - + -
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Residues in contact with PHE 8 (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 VAL* 4.1 9.6 - - + -
7C PHE* 1.3 99.4 - - - +
9C ASP* 1.3 61.9 + - - +
10C ILE* 3.4 28.3 + - + +
19C ARG* 3.1 4.0 - - - -
20C VAL* 2.8 36.0 + - + +
22C PHE* 3.5 29.8 - + + -
36C PHE* 3.3 31.2 - + - -
40C SER* 4.2 5.2 - - - -
48C TYR* 4.2 12.3 - + - -
53C PHE* 4.3 5.4 - + - -
112C PHE* 3.8 24.7 - + - -
114C ILE* 5.1 0.2 - - + -
158C ILE* 4.1 17.5 - - + -
160C ASP 3.5 3.8 - - - -
161C CYS* 3.8 13.9 - - + -
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Residues in contact with ASP 9 (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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7C PHE* 2.8 15.9 - - - -
8C PHE* 1.3 70.6 - - - +
10C ILE* 1.3 64.1 + - - +
18C GLY 3.6 5.1 - - - +
19C ARG* 2.7 51.2 + - - +
158C ILE* 4.8 0.6 - - - +
159C ALA* 3.0 32.0 + - + +
160C ASP* 2.7 30.3 + - + +
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Residues in contact with ILE 10 (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 PHE* 3.8 22.9 - - + +
9C ASP* 1.3 76.4 - - - +
11C ALA* 1.3 66.2 - - - +
16C PRO* 3.8 3.1 - - - +
17C LEU* 2.9 29.6 + - + -
18C GLY 2.9 14.4 + - - +
20C VAL* 4.1 24.2 - - + -
53C PHE* 3.8 24.9 - - + -
138C ILE* 4.7 6.7 - - + -
142C MET* 3.8 19.1 - - + -
156C ILE* 3.5 26.2 - - + -
157C THR 3.2 14.8 - - - +
158C ILE* 4.3 3.4 - - + -
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Residues in contact with ALA 11 (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 ILE* 1.3 78.9 - - - +
12C VAL* 1.3 62.5 + - - +
13C ASP 3.6 1.5 + - - -
14C GLY* 3.7 21.3 + - - +
15C GLU 3.3 13.0 - - - +
16C PRO* 4.2 2.9 - - + -
17C LEU 4.1 0.4 - - - +
155C LYS 3.1 3.8 - - - +
156C ILE* 3.6 1.2 - - - -
157C THR* 2.9 38.5 + - - +
159C ALA* 4.0 20.4 - - + -
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Residues in contact with VAL 12 (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 ILE* 5.2 1.6 - - + -
11C ALA* 1.3 71.6 - - - +
13C ASP* 1.3 69.4 + - + +
14C GLY 3.2 3.9 + - - -
15C GLU* 2.7 25.3 + - + +
17C LEU* 2.9 42.1 - - + +
145C PHE* 3.7 28.0 - - + -
154C LYS* 3.4 33.2 - - + -
155C LYS 3.6 3.1 - - - -
156C ILE* 3.8 11.0 - - + -
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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