Contacts of the strand formed by residues 100 - 106 (chain C) in PDB entry 2FBE
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 PHE 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C PHE* 4.8 4.3 - + - -
81C VAL 3.6 2.0 - - - -
82C CYS* 3.5 23.6 - - + -
86C VAL* 3.9 22.7 - - + -
87C ASN 4.5 5.2 - - - -
92C ILE* 4.4 16.2 - - + -
93C GLU* 3.5 25.8 - - + -
94C LEU* 3.4 24.7 - - + -
95C SER 2.9 18.8 + - - +
96C SER* 3.2 14.3 + - - +
98C HIS* 3.5 24.0 - - + -
99C GLY* 1.3 77.2 - - - +
101C LEU* 1.3 56.2 + - - +
102C THR* 4.4 5.6 - - + -
114C SER* 2.4 23.5 + - - +
167C PHE* 3.7 27.4 - + - -
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Residues in contact with LEU 101 (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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80C GLY* 3.4 2.8 - - - -
81C VAL* 2.9 40.9 + - + +
96C SER* 3.6 31.6 - - - +
99C GLY* 5.2 0.4 - - - -
100C PHE* 1.3 72.3 - - - +
102C THR* 1.3 60.4 + - - +
114C SER* 3.4 2.0 - - - -
141C ILE* 4.1 13.5 - - + -
143C PHE* 3.9 3.1 - - - -
155C PHE* 3.7 30.7 - - + -
158C ILE* 4.0 26.9 - - + -
159C PRO* 5.3 0.4 - - + -
164C TRP* 3.4 38.4 - - + -
4D GLY* 4.6 9.9 - - - +
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Residues in contact with THR 102 (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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78C ASP* 4.4 6.2 + - - +
79C VAL 3.1 19.3 - - - +
80C GLY* 3.8 4.0 - - - -
81C VAL 4.0 4.5 - - - +
94C LEU* 4.4 13.2 - - - +
100C PHE* 4.2 7.6 - - + -
101C LEU* 1.3 86.7 - - - +
103C VAL* 1.3 62.5 + - - +
112C ALA 4.7 0.2 - - - -
113C ALA* 3.4 2.4 - - - -
114C SER* 2.7 53.9 + - - -
143C PHE* 4.1 3.1 - - - -
155C PHE* 3.7 8.7 - - - -
167C PHE* 3.8 28.7 - - + -
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Residues in contact with VAL 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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77C TRP* 3.5 11.4 - - + -
78C ASP* 3.5 3.7 - - - -
79C VAL* 3.0 37.1 + - + -
102C THR* 1.3 76.2 - - - +
104C GLY* 1.3 62.4 + - - +
111C PHE* 6.2 1.1 - - + -
112C ALA 3.5 2.9 - - - -
113C ALA* 4.3 3.1 - - + -
121C LEU* 3.6 31.6 - - + -
127C LEU* 6.1 0.2 - - + -
130C VAL* 4.4 7.4 - - + -
143C PHE* 3.7 32.3 - - + -
152C ILE* 3.6 21.5 - - + -
153C TYR* 4.6 5.6 - - + -
155C PHE* 5.9 0.2 - - + -
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Residues in contact with GLY 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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77C TRP* 3.4 25.4 - - - -
78C ASP* 3.5 8.9 + - - -
103C VAL* 1.3 79.4 - - - +
105C CYS* 1.3 60.3 + - - -
106C ARG* 5.2 1.8 - - - -
111C PHE* 3.1 9.2 - - - +
112C ALA 2.8 35.0 + - - -
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Residues in contact with CYS 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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74C SER 5.7 0.4 - - - -
75C GLN 3.4 17.7 - - - +
76C VAL* 3.5 6.8 - - - +
77C TRP* 3.0 56.2 + - + +
78C ASP* 4.3 0.5 + - - +
104C GLY* 1.3 74.7 - - - -
106C ARG* 1.3 77.6 + - - +
109C LYS* 3.8 20.2 - - - -
110C VAL 3.3 5.4 - - - -
111C PHE* 3.8 22.4 - - + +
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Residues in contact with ARG 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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75C GLN 4.3 1.4 - - - +
76C VAL* 4.1 13.7 - - + -
78C ASP* 5.2 9.4 + - - +
94C LEU* 5.9 3.8 + - - +
104C GLY 5.2 1.6 - - - -
105C CYS* 1.3 84.0 - - - +
107C GLU* 1.3 70.9 + - - +
109C LYS* 2.9 18.9 + - - -
110C VAL* 2.6 25.6 + - + +
112C ALA* 4.9 8.7 - - + -
118C MSE 3.4 35.2 - - - +
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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