Contacts of the strand formed by residues 102 - 107 (chain C) in PDB entry 5FFO
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 102 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C SER* 1.3 81.3 - - - +
103C TYR* 1.3 71.9 + - - +
104C MET* 4.2 18.6 - - + +
189C ARG* 3.8 0.5 - - - -
190C LEU* 2.7 52.4 + - + +
210C PHE* 3.6 26.0 - - + -
215C ARG* 3.6 34.1 - - + +
218C LEU* 4.9 0.7 - - + -
219C ALA* 3.6 33.9 - - + +
221C ILE* 4.8 8.7 - - + -
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Residues in contact with TYR 103 (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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84C MET* 5.3 2.4 - - - +
91C ILE* 5.1 7.3 - - + +
95C PHE* 3.5 52.3 - + + -
96C LYS* 4.4 7.2 - - - -
98C SER* 2.3 39.7 + - - -
101C SER* 3.9 15.5 + - - -
102C ILE* 1.3 76.9 - - - +
104C MET* 1.3 67.2 + - - +
105C PHE* 4.3 16.9 - - + -
150C TRP* 4.4 7.4 - + - -
188C PHE 3.9 3.6 - - - +
189C ARG* 3.8 39.7 + - + -
215C ARG* 4.4 23.1 + - - +
221C ILE* 6.1 0.3 - - - +
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Residues in contact with MET 104 (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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84C MET* 4.3 19.7 - - - -
102C ILE* 4.2 15.7 + - + -
103C TYR* 1.3 78.3 - - - +
105C PHE* 1.3 63.6 + - - +
106C PHE* 4.5 13.0 - - + -
126C LEU* 3.9 20.4 - - + -
128C LEU* 3.9 30.5 - - + -
141C LEU* 5.0 2.9 - - + -
187C GLY* 3.3 1.8 - - - -
188C PHE* 2.7 61.9 + - + +
189C ARG 4.8 0.4 - - - +
190C LEU* 4.6 21.1 - - + +
227C PRO* 4.2 13.0 - - + -
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Residues in contact with PHE 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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84C MET* 3.7 5.0 - - - +
85C VAL* 3.3 31.3 + - + +
91C ILE* 3.7 38.5 - - + +
95C PHE* 3.3 45.5 - + - -
103C TYR* 4.3 9.9 - - + -
104C MET* 1.3 91.2 - - - +
106C PHE* 1.3 68.8 + - - +
144C LYS* 3.2 39.7 - - + -
150C TRP* 4.4 5.2 - + - -
185C ILE* 3.8 15.0 - - + -
186C GLU 3.1 17.9 - - - -
187C GLY* 4.0 1.3 - - - -
188C PHE 4.6 4.0 - - - -
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Residues in contact with PHE 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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82C VAL* 3.9 18.6 - - + -
83C LEU 3.5 20.2 - - - -
84C MET* 3.6 27.6 - - + -
85C VAL* 4.3 5.8 - - - -
104C MET* 4.5 13.0 - - + -
105C PHE* 1.3 81.8 - - - +
107C GLN* 1.3 68.9 + - - +
111C LEU* 4.7 14.6 - - + -
126C LEU* 4.1 21.3 - - + -
178C TRP* 5.4 3.8 - + + -
185C ILE* 3.7 9.4 - - - +
186C GLU* 3.4 29.7 + - + +
187C GLY* 4.9 2.7 - - - -
188C PHE* 4.0 33.2 - + - -
227C PRO* 4.4 6.1 - - + -
229C LEU* 4.4 13.5 - - + -
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Residues in contact with GLN 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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85C VAL* 4.4 19.4 - - + +
89C ASN* 5.1 12.3 - - - +
106C PHE* 1.3 78.1 - - - +
108C THR* 1.3 63.5 + - - +
109C SER* 3.3 10.7 + - - +
110C GLU* 3.4 35.6 + - + +
111C LEU* 3.5 23.3 + - - +
184C GLU 4.1 7.9 - - - +
185C ILE* 5.9 3.1 - - + -
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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