Contacts of the strand formed by residues 106 - 111 (chain I) in PDB entry 5TJ4
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79I ILE* 2.9 50.9 - - + +
81I PRO* 4.5 3.3 - - + -
85I PHE* 3.8 15.5 - + - -
94I TRP* 4.3 5.6 - + - -
105I ALA* 1.3 71.9 - - - +
107I PRO* 1.3 67.0 - - + +
108I ILE* 3.5 7.4 - - + +
263I SER* 3.2 2.8 - - - -
264I ALA* 2.7 42.5 + - + +
266I ILE* 4.2 5.6 - - + -
277I LYS* 3.3 15.7 - - + +
280I LEU* 3.6 29.2 - - + -
281I GLU* 2.8 42.8 + - + -
285I LEU* 3.9 27.4 - - + -
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Residues in contact with PRO 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89I LEU* 3.9 8.0 - - + +
93I THR* 3.5 51.8 - - - +
94I TRP* 3.5 30.3 - - + -
97I VAL* 3.7 9.4 - - + -
105I ALA 3.5 4.2 - - - +
106I TYR* 1.3 82.7 - - - +
108I ILE* 1.3 64.7 + - - +
261I VAL* 3.9 8.3 - - + -
262I LEU 4.0 0.2 - - - +
263I SER* 3.9 10.3 - - - +
285I LEU* 3.6 13.5 - - - +
303I ALA* 3.7 7.2 - - + +
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Residues in contact with ILE 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I PHE* 3.9 20.2 - - + -
106I TYR* 3.5 17.5 - - + +
107I PRO* 1.3 78.6 - - - +
109I ALA* 1.3 64.2 + - + +
262I LEU* 2.8 36.1 + - + +
263I SER* 4.2 0.9 - - - -
264I ALA* 4.1 15.9 - - + +
280I LEU* 5.2 0.2 - - + -
284I LEU* 4.2 16.8 - - + -
285I LEU* 4.0 21.5 - - + +
290I LEU* 3.9 25.0 - - + +
299I LEU* 4.4 8.3 - - + -
302I VAL* 3.7 5.4 - - - +
303I ALA* 2.8 23.3 + - - +
304I LEU 4.5 1.0 + - - -
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Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ILE* 1.3 87.5 - - + +
110I VAL* 1.3 64.7 + - - +
111I GLU* 5.4 0.2 - - - -
261I VAL* 3.2 6.4 - - - +
262I LEU* 2.7 39.2 + - + +
299I LEU* 3.7 39.9 - - + +
301I ALA 3.6 10.5 - - - +
302I VAL* 3.8 4.9 - - + -
303I ALA* 3.9 4.2 - - - +
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Residues in contact with VAL 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I TYR* 6.4 0.2 - - + -
92I PHE* 3.8 34.8 - - + -
93I THR* 4.1 13.7 - - + -
109I ALA* 1.3 76.2 - - - +
111I GLU* 1.3 66.8 + - - +
112I ALA* 5.7 0.2 - - + -
259I VAL* 5.1 7.6 - - + -
260I GLY 3.5 8.7 - - - +
261I VAL* 4.4 10.5 - - + +
299I LEU 4.4 0.9 - - - -
300I GLY* 3.7 4.0 - - - -
301I ALA* 2.7 45.8 + - + +
302I VAL 5.2 2.9 - - - +
320I THR* 4.6 4.4 - - + +
321I MET* 4.8 14.1 - - + -
324I ALA* 4.9 11.4 - - + -
329I ILE* 6.1 1.1 - - + -
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Residues in contact with GLU 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I ALA* 4.2 8.0 - - - +
109I ALA 5.2 0.4 - - - +
110I VAL* 1.3 77.7 - - - +
112I ALA* 1.3 64.2 + - - +
155I TYR* 3.9 5.5 + - - +
229I PRO* 4.5 7.4 - - + -
230I TRP* 3.7 26.4 - - + -
259I VAL* 3.8 2.6 - - - +
260I GLY* 2.9 44.7 + - - +
262I LEU* 3.8 31.6 - - - +
299I LEU 4.1 15.8 - - - +
320I THR* 4.8 0.7 - - - -
1S GLC 2.6 40.5 + - - -
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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