Contacts of the strand formed by residues 106 - 112 (chain C) in PDB entry 3IOT
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 TYR 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C ILE* 3.5 46.6 - - + +
80C THR 4.4 1.4 + - - -
81C PRO* 4.1 16.8 - - + -
85C PHE* 4.5 4.3 - + - -
94C TRP* 4.1 12.3 - + - -
105C ALA* 1.3 70.8 - - - +
107C PRO* 1.3 70.3 - - + +
108C ILE* 3.6 3.5 + - + +
263C SER* 3.2 3.6 - - - -
264C ALA* 2.8 43.8 + - + +
266C ILE* 4.8 2.5 - - + -
277C LYS* 3.6 20.5 - - - +
280C LEU* 3.6 43.1 - - + -
281C GLU* 2.9 31.8 + - + +
285C LEU* 3.8 20.2 - - + -
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Residues in contact with PRO 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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89C LEU* 3.8 12.8 - - + +
93C THR* 3.7 46.2 - - - +
94C TRP* 3.5 23.1 - - + -
97C VAL* 3.8 9.6 - - + -
105C ALA 3.7 2.9 - - - +
106C TYR* 1.3 85.3 - - - +
108C ILE* 1.3 65.2 + - - +
261C VAL* 4.3 10.1 - - + -
262C LEU 3.8 5.2 - - - +
263C SER* 4.4 2.9 - - - +
285C LEU* 3.6 15.6 - - - +
303C ALA* 3.8 13.4 - - + +
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Residues in contact with ILE 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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61C PHE* 3.8 33.0 - - + -
106C TYR* 3.7 11.9 - - + +
107C PRO* 1.3 83.3 - - - +
109C ALA* 1.3 63.2 + - + +
261C VAL* 4.4 0.4 - - - +
262C LEU* 2.7 36.7 + - + +
263C SER* 4.1 0.4 - - - -
264C ALA* 4.0 9.4 - - + +
280C LEU* 5.6 0.7 - - + -
284C LEU* 4.1 15.5 - - + -
285C LEU* 4.3 17.6 - - + +
290C LEU* 4.4 19.6 - - + +
293C VAL* 6.5 0.2 - - + -
299C LEU* 4.8 10.1 - - + -
302C VAL* 3.6 7.8 - - - +
303C ALA* 3.0 24.9 + - - +
304C LEU 4.9 0.2 + - - -
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Residues in contact with ALA 109 (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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108C ILE* 1.3 86.4 - - + +
110C VAL* 1.3 64.3 + - - +
260C GLY 3.8 0.5 - - - +
261C VAL* 3.2 7.2 - - - +
262C LEU* 2.9 37.1 + - + +
299C LEU* 3.3 38.1 - - + +
301C ALA 3.3 6.7 - - - +
302C VAL* 4.2 2.0 - - + +
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Residues in contact with VAL 110 (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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92C PHE* 4.3 7.0 - - + -
93C THR* 4.1 24.9 - - + -
109C ALA* 1.3 76.3 - - - +
111C GLU* 1.3 65.3 + - - +
229C PRO* 5.6 0.9 - - - +
259C VAL* 3.6 16.4 - - + -
260C GLY 3.9 1.3 - - - -
261C VAL* 4.3 8.1 - - + -
299C LEU 4.5 3.3 - - - +
300C GLY* 5.0 0.7 - - - -
301C ALA* 2.8 32.8 + - + +
302C VAL 4.4 9.0 - - - -
303C ALA* 4.5 1.3 - - + +
320C THR* 4.2 5.0 - - + +
321C MET* 3.9 26.9 - - + -
324C ALA* 3.6 30.5 - - + -
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Residues in contact with GLU 111 (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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110C VAL* 1.3 78.3 - - - +
112C ALA* 1.3 65.0 + - - +
155C TYR* 4.9 4.1 + - - +
229C PRO* 3.8 25.6 - - + +
230C TRP* 3.5 33.9 + - + +
258C PHE 3.8 0.7 - - - +
259C VAL* 3.4 4.7 - - - +
260C GLY* 2.8 49.6 + - - +
320C THR* 4.5 1.1 - - - -
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Residues in contact with ALA 112 (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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111C GLU* 1.3 79.1 - - - +
113C LEU* 1.3 69.2 + - - +
114C SER* 3.7 7.8 + - - -
155C TYR* 4.9 3.1 - - - -
228C GLY* 4.2 0.8 - - - -
229C PRO* 3.8 17.6 - - - +
230C TRP* 5.5 0.7 - - - -
257C PRO* 4.6 3.8 - - + -
258C PHE 3.9 13.7 - - - +
259C VAL* 4.8 1.1 - - + -
320C THR* 3.8 18.4 + - - +
323C ASN 4.4 1.6 - - - -
324C ALA* 3.8 34.1 - - + +
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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