Contacts of the strand formed by residues 104 - 108 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.5 0.7 - - + -
52C VAL 4.1 0.2 - - - +
53C VAL* 3.5 5.0 - - - +
54C SER* 2.8 44.9 + - - +
55C ALA 3.6 14.6 - - - +
56C ALA* 3.4 15.3 - - + +
58C CYS* 4.2 8.3 - - + +
59C TYR* 3.6 44.4 - - - +
63C ILE* 4.6 2.5 - - + -
88C SER* 4.8 3.4 - - - -
89C ILE 3.4 17.9 - - - +
90C VAL* 3.8 9.2 - - + +
103C ILE* 1.3 77.4 - - - +
105C LEU* 1.3 71.0 + - - +
106C ILE* 3.7 31.4 - - + -
237C TRP* 4.5 0.9 - - - -
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Residues in contact with LEU 105 (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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47C ILE* 4.5 3.1 - - + -
51C TRP* 3.8 18.6 - - + -
52C VAL 3.5 3.1 - - - +
53C VAL* 3.8 33.7 - - + +
87C LYS 4.0 0.9 - - - +
88C SER* 3.6 0.9 - - - -
89C ILE* 2.7 45.5 + - + +
104C MET* 1.3 72.7 - - - +
106C ILE* 1.3 60.6 + - - +
237C TRP* 3.6 28.7 - - + -
238C ILE* 3.8 31.4 - - + +
241C THR* 3.7 28.7 - - + -
242C ILE* 4.5 8.1 - - + -
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Residues in contact with ILE 106 (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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33C LEU* 3.7 32.5 - - + -
51C TRP* 3.3 8.4 - - - -
52C VAL* 2.7 55.2 + - + +
54C SER* 4.6 3.4 - - - -
63C ILE* 4.6 7.9 - - + -
65C VAL* 4.3 13.7 - - + -
85C ALA* 3.6 28.3 - - + -
87C LYS 3.6 3.8 - - - +
88C SER* 4.7 6.5 - - - +
104C MET* 3.7 32.1 - - + +
105C LEU* 1.3 78.5 - - - +
107C LYS* 1.3 65.7 + - - +
108C LEU* 4.1 1.5 + - + -
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Residues in contact with LYS 107 (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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50C GLN* 3.4 36.8 + - + +
51C TRP* 3.6 32.6 - - + +
85C ALA* 3.3 3.6 - - - -
86C SER* 2.6 37.0 + - - -
87C LYS* 2.8 38.9 + - + +
106C ILE* 1.3 75.1 - - - +
108C LEU* 1.3 63.4 + - - +
245C ASN* 2.7 35.3 + - - +
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Residues in contact with LEU 108 (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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46C LEU* 4.6 1.3 - - + -
49C SER 3.7 21.8 - - - +
50C GLN* 2.9 32.9 + - - +
52C VAL* 4.0 20.0 - - + -
65C VAL* 3.4 39.5 - - + -
67C LEU* 4.3 6.1 - - + -
83C ILE* 3.7 19.1 - - + -
84C SER 3.6 3.8 - - - +
86C SER* 4.0 1.8 - - - -
106C ILE* 4.6 2.5 - - + -
107C LYS* 1.3 79.3 - - - +
109C LYS* 1.3 68.2 + - - +
110C SER 2.9 18.6 + - - +
112C ALA* 3.8 16.8 - - + -
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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