Contacts of the strand formed by residues 78 - 83 (chain L) in PDB entry 4M75
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 78 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22L ILE* 3.8 24.9 - - + -
23L VAL 4.4 0.2 - - - -
24L LEU* 4.2 7.0 - - + -
41L VAL 3.6 20.9 - - - +
43L VAL* 3.7 27.6 - - + +
73L LEU* 4.5 5.6 - - + +
74L SER 4.0 5.4 - - - +
75L GLY* 3.3 23.9 + - - +
76L ASN 3.3 0.2 - - - -
77L ASN* 1.3 77.7 - - - +
79L ALA* 1.3 61.7 + - - +
80L ILE 4.7 1.1 - - - +
81L LEU* 3.9 20.2 - - + -
95M ARG* 3.5 34.9 + - + +
98M ILE* 3.8 13.8 - - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L VAL* 3.0 17.4 + - + +
24L LEU 4.1 2.2 - - - +
25L GLN* 4.0 21.3 - - + +
77L ASN 3.3 1.4 + - - -
78L ILE* 1.3 71.6 - - - +
80L ILE* 1.3 63.5 + - + +
42M LEU* 4.2 15.9 - - + -
46M LYS* 5.8 2.7 - - + -
94M ILE* 3.7 2.4 - - - +
95M ARG* 2.8 34.2 + - - +
98M ILE* 4.1 21.9 - - + +
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Residues in contact with ILE 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L ILE* 3.9 2.9 - - - +
23L VAL* 3.0 54.0 + - + +
78L ILE* 4.7 0.6 - - - +
79L ALA* 1.3 82.7 + - + +
81L LEU* 1.3 64.8 + - - +
82L VAL* 5.0 2.0 - - + -
42M LEU* 4.7 11.4 - - + -
46M LYS* 5.9 3.4 - - + -
48M VAL* 5.4 8.3 - - + -
66M THR* 6.5 0.2 - - - -
68M GLU* 4.3 24.9 - - + +
89M LEU* 4.4 13.5 - - + -
92M THR* 4.1 14.4 - - + -
93M VAL 3.3 10.1 - - - +
94M ILE* 3.1 35.4 - - + -
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Residues in contact with LEU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 3.8 39.5 - - + -
20L VAL* 5.2 5.8 - - + -
21L LEU 3.7 3.6 - - - +
22L ILE* 3.6 27.1 - - + -
34L LEU* 5.4 4.7 - - + -
41L VAL* 4.6 4.5 - - + -
43L VAL* 4.3 16.4 - - + -
78L ILE* 3.9 20.6 - - + -
80L ILE* 1.3 73.9 - - - +
82L VAL* 1.3 60.3 + - - +
83L PRO* 3.8 4.8 - - + +
92M THR* 3.3 8.7 - - - -
93M VAL* 2.7 45.6 + - + +
95M ARG* 4.1 17.9 - - + -
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Residues in contact with VAL 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L VAL* 3.3 4.0 - - - +
21L LEU* 2.5 61.1 + - + +
23L VAL* 4.6 8.7 - - + -
80L ILE* 5.0 2.5 - - + +
81L LEU* 1.3 80.9 - - - +
83L PRO* 1.3 74.0 - - - +
85L GLY 4.5 12.1 - - - +
89M LEU* 4.3 26.7 - - + -
90M GLY 4.9 4.7 - - - +
91M LEU 4.1 12.1 - - - +
92M THR* 3.7 17.0 - - + -
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Residues in contact with PRO 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L VAL* 4.8 13.9 - - + -
12L ILE* 6.2 0.2 - - - -
15L THR* 3.7 33.4 - - + +
18L GLN* 5.9 0.4 - - + -
19L LYS 3.6 0.9 - - - +
20L VAL* 3.7 10.1 - - + -
81L LEU* 3.8 8.7 - - + +
82L VAL* 1.3 95.5 - - - +
84L GLY* 1.3 58.4 + - - +
85L GLY 3.8 1.2 + - - -
91M LEU* 4.0 17.6 - - + +
92M THR* 4.9 1.1 - - - -
93M VAL* 5.4 2.0 - - + +
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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