Contacts of the strand formed by residues 104 - 108 (chain F) in PDB entry 1C9T
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 MET 104 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 4.6 1.6 - - + -
53F VAL* 3.6 6.2 - - - +
54F SER* 2.7 45.0 + - - +
55F ALA 3.3 18.6 - - - +
56F ALA* 3.5 13.7 - - + +
58F CYS* 3.9 6.3 - - + +
59F TYR* 3.5 49.6 - - - +
63F ILE* 4.6 1.8 - - + -
88F SER* 4.9 2.7 - - - -
89F ILE 3.5 21.3 - - - +
90F VAL* 3.9 2.7 - - + -
103F ILE* 1.3 74.7 - - - +
105F LEU* 1.3 71.9 + - - +
106F ILE* 4.0 26.9 - - + -
237F TRP* 4.6 0.9 - - - -
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ILE* 4.5 3.1 - - + -
51F TRP* 3.8 18.4 - - + -
52F VAL 3.7 2.0 - - - +
53F VAL* 3.9 24.5 - - + +
87F LYS 3.9 0.9 - - - +
88F SER* 3.6 1.0 - - - -
89F ILE* 2.8 47.5 + - + +
104F MET* 1.3 78.1 - - - +
106F ILE* 1.3 61.3 + - - +
237F TRP* 3.7 17.0 - - + -
238F ILE* 3.7 42.6 - - + +
241F THR* 3.7 31.0 - - + -
242F ILE* 4.5 8.7 - - + -
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Residues in contact with ILE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.7 39.5 - - + -
51F TRP* 3.2 8.9 - - - -
52F VAL* 2.7 54.3 + - + +
54F SER* 4.6 4.5 - - - -
63F ILE* 4.4 10.5 - - + -
65F VAL* 4.4 12.1 - - + -
85F ALA* 3.4 29.8 - - + -
87F LYS 3.6 4.5 - - - +
88F SER* 4.5 8.3 - - - +
104F MET* 4.0 22.4 - - + -
105F LEU* 1.3 77.7 - - - +
107F LYS* 1.3 65.7 + - - +
108F LEU* 4.1 1.5 + - + +
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Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLN* 2.8 37.9 + - - +
111B ALA* 4.5 4.6 - - - +
50F GLN* 3.5 30.1 - - - +
51F TRP* 3.6 29.3 - - + +
85F ALA* 3.3 4.7 - - - -
86F SER* 2.6 38.0 + - - -
87F LYS* 2.8 39.9 + - + +
106F ILE* 1.3 74.5 - - - +
108F LEU* 1.3 61.5 + - - +
245F ASN 2.9 28.7 + - - +
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 4.5 3.1 - - + -
49F SER 3.5 23.6 - - - +
50F GLN* 2.9 31.3 + - - +
52F VAL* 4.0 20.9 - - + -
65F VAL* 3.4 39.3 - - + -
67F LEU* 4.5 4.3 - - + -
83F ILE* 3.8 17.9 - - + -
84F SER 3.7 3.8 - - - +
85F ALA* 5.1 0.2 - - - -
86F SER* 4.1 1.4 - - - -
106F ILE* 4.7 2.0 - - + -
107F LYS* 1.3 77.2 - - - +
109F LYS* 1.3 68.4 + - - +
110F SER 2.9 21.6 + - - +
112F ALA* 3.9 17.0 - - + -
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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